I think Apple would actually prefer App Extensions to use the same bundle version as the app they are contained in. This is the email I have been getting from iTunes Connect with every submission:
We have discovered one or more issues with your recent delivery for
"Awesome App". Your delivery was successful, but you may wish to
correct the following issues in your next delivery:
CFBundleVersion Mismatch - The CFBundleVersion value '94' of extension
'Awesome App.app/PlugIns/Awesome App Today Extension.appex' does not
match the CFBundleVersion value '99' of its containing iOS application
'Awesome App.app'.
CFBundleShortVersionString Mismatch - The CFBundleShortVersionString
value '1.0' of extension 'Awesome App.app/PlugIns/Awesome App Today
Extension.appex' does not match the CFBundleShortVersionString value
'1.3.0' of its containing iOS application 'Awesome App.app'.
After you’ve corrected the issues, you can use Xcode or Application
Loader to upload a new binary to iTunes Connect.
I can ignore these warnings and the build passes review but this is either a bug in iTunes Connect or the numbers should be the same. This doesn't actually make sense since the extension won't necessarily be updated at the same rate of the app. Anyways