I think what you might need to do is to first create an ItemContainerStyle for a TreeViewItem, then in the style, replace the ContentPresenter inside the Header button with a ContentControl (inherits from Control which allows IsTabStop). Then you should be able to tab thru controls in your StackPanel without setting any tab index.
Please give it a try and let me know if it helps. :)
ItemContainerStyle:
<Style TargetType="sdk:TreeViewItem">
<Setter Property="Padding" Value="3"/>
<Setter Property="HorizontalContentAlignment" Value="Left"/>
<Setter Property="VerticalContentAlignment" Value="Top"/>
<Setter Property="Background" Value="Transparent"/>
<Setter Property="BorderThickness" Value="1"/>
<Setter Property="Cursor" Value="Arrow"/>
<Setter Property="IsTabStop" Value="False"/>
<Setter Property="TabNavigation" Value="Once"/>
<Setter Property="Margin" Value="0 1 0 0"/>
<Setter Property="Template">
<Setter.Value>
<ControlTemplate TargetType="sdk:TreeViewItem">
<Grid Background="{x:Null}">
<Grid.ColumnDefinitions>
<ColumnDefinition Width="15"/>
<ColumnDefinition Width="Auto"/>
<ColumnDefinition Width="*"/>
</Grid.ColumnDefinitions>
<Grid.RowDefinitions>
<RowDefinition Height="Auto"/>
<RowDefinition Height="*"/>
</Grid.RowDefinitions>
<VisualStateManager.VisualStateGroups>
<VisualStateGroup x:Name="CommonStates">
<VisualState x:Name="Normal"/>
<VisualState x:Name="MouseOver"/>
<VisualState x:Name="Pressed"/>
<VisualState x:Name="Disabled">
<Storyboard>
<ObjectAnimationUsingKeyFrames Duration="0" Storyboard.TargetProperty="Foreground" Storyboard.TargetName="Header">
<DiscreteObjectKeyFrame KeyTime="0">
<DiscreteObjectKeyFrame.Value>
<SolidColorBrush Color="#FF999999"/>
</DiscreteObjectKeyFrame.Value>
</DiscreteObjectKeyFrame>
</ObjectAnimationUsingKeyFrames>
</Storyboard>
</VisualState>
</VisualStateGroup>
<VisualStateGroup x:Name="SelectionStates">
<VisualState x:Name="Unselected"/>
<VisualState x:Name="Selected">
<Storyboard>
<DoubleAnimation Duration="0" To=".75" Storyboard.TargetProperty="Opacity" Storyboard.TargetName="Selection"/>
</Storyboard>
</VisualState>
<VisualState x:Name="SelectedInactive">
<Storyboard>
<DoubleAnimation Duration="0" To=".2" Storyboard.TargetProperty="Opacity" Storyboard.TargetName="Selection"/>
<ColorAnimation Duration="0" To="#FF999999" Storyboard.TargetProperty="Color" Storyboard.TargetName="SelectionFill"/>
<ColorAnimation Duration="0" To="#FF333333" Storyboard.TargetProperty="Color" Storyboard.TargetName="SelectionStroke"/>
</Storyboard>
</VisualState>
</VisualStateGroup>
<VisualStateGroup x:Name="HasItemsStates">
<VisualState x:Name="HasItems"/>
<VisualState x:Name="NoItems">
<Storyboard>
<ObjectAnimationUsingKeyFrames Duration="0" Storyboard.TargetProperty="Visibility" Storyboard.TargetName="ExpanderButton">
<DiscreteObjectKeyFrame KeyTime="0" Value="Collapsed"/>
</ObjectAnimationUsingKeyFrames>
</Storyboard>
</VisualState>
</VisualStateGroup>
<VisualStateGroup x:Name="ExpansionStates">
<VisualState x:Name="Collapsed"/>
<VisualState x:Name="Expanded">
<Storyboard>
<ObjectAnimationUsingKeyFrames Duration="0" Storyboard.TargetProperty="Visibility" Storyboard.TargetName="ItemsHost">
<DiscreteObjectKeyFrame KeyTime="0" Value="Visible"/>
</ObjectAnimationUsingKeyFrames>
</Storyboard>
</VisualState>
</VisualStateGroup>
<VisualStateGroup x:Name="ValidationStates">
<VisualState x:Name="Valid"/>
<VisualState x:Name="InvalidUnfocused">
<Storyboard>
<ObjectAnimationUsingKeyFrames Storyboard.TargetProperty="Visibility" Storyboard.TargetName="Validation">
<DiscreteObjectKeyFrame KeyTime="0" Value="Visible"/>
</ObjectAnimationUsingKeyFrames>
</Storyboard>
</VisualState>
<VisualState x:Name="InvalidFocused">
<Storyboard>
<ObjectAnimationUsingKeyFrames Storyboard.TargetProperty="Visibility" Storyboard.TargetName="Validation">
<DiscreteObjectKeyFrame KeyTime="0" Value="Visible"/>
</ObjectAnimationUsingKeyFrames>
<ObjectAnimationUsingKeyFrames Storyboard.TargetProperty="IsOpen" Storyboard.TargetName="ValidationToolTip">
<DiscreteObjectKeyFrame KeyTime="0">
<DiscreteObjectKeyFrame.Value>
<System:Boolean>True</System:Boolean>
</DiscreteObjectKeyFrame.Value>
</DiscreteObjectKeyFrame>
</ObjectAnimationUsingKeyFrames>
</Storyboard>
</VisualState>
</VisualStateGroup>
</VisualStateManager.VisualStateGroups>
<ToggleButton x:Name="ExpanderButton" HorizontalAlignment="Stretch" IsTabStop="False" TabNavigation="Once" VerticalAlignment="Stretch">
<ToggleButton.Template>
<ControlTemplate TargetType="ToggleButton">
<Grid x:Name="Root" Background="Transparent">
<VisualStateManager.VisualStateGroups>
<VisualStateGroup x:Name="CommonStates">
<VisualState x:Name="Normal"/>
<VisualState x:Name="MouseOver">
<Storyboard>
<ColorAnimation Duration="0" To="#FF1BBBFA" Storyboard.TargetProperty="(Path.Stroke).Color" Storyboard.TargetName="UncheckedVisual"/>
</Storyboard>
</VisualState>
<VisualState x:Name="Disabled">
<Storyboard>
<DoubleAnimation Duration="0" To=".7" Storyboard.TargetProperty="Opacity" Storyboard.TargetName="Root"/>
</Storyboard>
</VisualState>
</VisualStateGroup>
<VisualStateGroup x:Name="CheckStates">
<VisualState x:Name="Unchecked"/>
<VisualState x:Name="Checked">
<Storyboard>
<DoubleAnimation Duration="0" To="0" Storyboard.TargetProperty="Opacity" Storyboard.TargetName="UncheckedVisual"/>
<DoubleAnimation Duration="0" To="1" Storyboard.TargetProperty="Opacity" Storyboard.TargetName="CheckedVisual"/>
</Storyboard>
</VisualState>
</VisualStateGroup>
</VisualStateManager.VisualStateGroups>
<Grid HorizontalAlignment="Right" Margin="2 2 5 2">
<Path x:Name="UncheckedVisual" Data="M 0,0 L 0,9 L 5,4.5 Z" Fill="#FFFFFFFF" HorizontalAlignment="Right" Height="9" Stroke="#FF989898" StrokeThickness="1" StrokeLineJoin="Miter" VerticalAlignment="Center" Width="6"/>
<Path x:Name="CheckedVisual" Data="M 6,0 L 6,6 L 0,6 Z" Fill="#FF262626" HorizontalAlignment="Center" Height="6" Opacity="0" StrokeLineJoin="Miter" VerticalAlignment="Center" Width="6"/>
</Grid>
</Grid>
</ControlTemplate>
</ToggleButton.Template>
</ToggleButton>
<Rectangle x:Name="Selection" Grid.Column="1" IsHitTestVisible="False" Opacity="0" RadiusY="2" RadiusX="2" StrokeThickness="1">
<Rectangle.Fill>
<SolidColorBrush x:Name="SelectionFill" Color="#FFBADDE9"/>
</Rectangle.Fill>
<Rectangle.Stroke>
<SolidColorBrush x:Name="SelectionStroke" Color="#FF6DBDD1"/>
</Rectangle.Stroke>
</Rectangle>
<Button x:Name="Header" BorderBrush="{TemplateBinding BorderBrush}" BorderThickness="{TemplateBinding BorderThickness}" Background="{TemplateBinding Background}" Cursor="{TemplateBinding Cursor}" ClickMode="Hover" Grid.Column="1" Foreground="{TemplateBinding Foreground}" HorizontalAlignment="{TemplateBinding HorizontalContentAlignment}" IsTabStop="False" TabNavigation="Once" VerticalAlignment="{TemplateBinding VerticalContentAlignment}">
<Button.Template>
<ControlTemplate TargetType="Button">
<Grid Background="{TemplateBinding Background}">
<VisualStateManager.VisualStateGroups>
<VisualStateGroup x:Name="CommonStates">
<VisualState x:Name="Normal"/>
<VisualState x:Name="Pressed">
<Storyboard>
<DoubleAnimation Duration="0" To=".5" Storyboard.TargetProperty="Opacity" Storyboard.TargetName="Hover"/>
</Storyboard>
</VisualState>
<VisualState x:Name="Disabled">
<Storyboard>
<DoubleAnimation Duration="0" To=".55" Storyboard.TargetProperty="Opacity" Storyboard.TargetName="Content"/>
</Storyboard>
</VisualState>
</VisualStateGroup>
</VisualStateManager.VisualStateGroups>
<Rectangle x:Name="Hover" Fill="#FFBADDE9" IsHitTestVisible="False" Opacity="0" RadiusY="2" RadiusX="2" Stroke="#FF6DBDD1" StrokeThickness="1"/>
<ContentControl x:Name="Content" Cursor="{TemplateBinding Cursor}" ContentTemplate="{TemplateBinding ContentTemplate}" Content="{TemplateBinding Content}" HorizontalAlignment="Left" Margin="{TemplateBinding Padding}" IsTabStop="False"/>
</Grid>
</ControlTemplate>
</Button.Template>
<ContentPresenter ContentTemplate="{TemplateBinding HeaderTemplate}" Content="{TemplateBinding Header}"/>
</Button>
<Border x:Name="Validation" BorderBrush="#FFDB000C" BorderThickness="{TemplateBinding BorderThickness}" Grid.Column="1" CornerRadius="2" Visibility="Collapsed">
<ToolTipService.ToolTip>
<ToolTip x:Name="ValidationToolTip" DataContext="{Binding RelativeSource={RelativeSource TemplatedParent}}" IsHitTestVisible="True" Placement="Right" PlacementTarget="{Binding ElementName=Header}" Template="{StaticResource CommonValidationToolTipTemplate}"/>
</ToolTipService.ToolTip>
<Grid Background="Transparent" HorizontalAlignment="Right" Height="10" Margin="0,-4,-4,0" VerticalAlignment="Top" Width="10">
<Path Data="M 1,0 L6,0 A 2,2 90 0 1 8,2 L8,7 Z" Fill="#FFDC000C" Margin="-1,3,0,0"/>
<Path Data="M 0,0 L2,0 L 8,6 L8,8" Fill="#FFFFFFFF" Margin="-1,3,0,0"/>
</Grid>
</Border>
<ItemsPresenter x:Name="ItemsHost" Grid.ColumnSpan="2" Grid.Column="1" Grid.Row="1" Visibility="Collapsed"/>
</Grid>
</ControlTemplate>
</Setter.Value>
</Setter>
</Style>
