The attributes and elements that Swiper decides to 'swipe' away is controlled by using an xslt file.
The default xslt file does indeed choose DesignerVersion and $$ScriptName to be swiped.
DesignerVersion is swiped by default, because this will cause a lot of merge conflicts when you upgrade domino designer, or if one of your colleagues decides to install a fixpack that you didn't all of a sudden every file will have a conflict again that needs to be resolved.
Although there may be the argument that import/export behaviour may be different for each version, I would be skeptical to hear that IBM have made any changes to DXL importing / exporting in the last few years.
Regarding $$ScriptName, to be honest I can't remember why I included that to be swiped but it must have been annoying me. It hasn't caused any problem for me, but then again I don't do a lot of classic NSF development so maybe that actually does cause a problem when doing that.
Providing your own custom xslt filter:
If you don't want these 'swiped' then you can provide a customised xslt file
Make a copy of the default file org.openntf.swiper/src/org/openntf/swiper/action/DXLClean.xsl
Then comment or remove the entries related to Designer version (there are more than one)
<xsl:template match="//n:form/@replicaid"/>
<xsl:template match="//n:form/@version"/>
<!--<xsl:template match="//n:form/@designerversion"/>-->
<xsl:template match="//n:database/@replicaid"/>
<xsl:template match="//n:database/@version"/>
<!--<xsl:template match="//n:database/@designerversion"/>-->
.... and so on make sure you do all of them
Then comment out / remove the one for $$ScriptName
<!-- Ignore the DesignerVersion Item and this random FileModDT one -->
<xsl:template match="//n:item[@name='$DesignerVersion']"/>
<!--<xsl:template match="//n:item[@name='$$ScriptName']"/>-->
<xsl:template match="//n:item[@name='$ScriptLib_error']"/>
<xsl:template match="//n:imageresource/n:item[@name='$FileModDT']"/>
<xsl:template match="//n:imageresource/n:item[@name='$EditFilePath']"/>
Save this as a .xsl file somewhere
Then in Designer go to File -> Preferences -> Swiper
Under 'Custom XSLT Filter' browse to the location of your file and click apply / ok.
These rules will then take affect the next time swiper runs when a file is exported from NSF to the ODP. So you may need to force a save of a file, or deliberately 'swipe' a file to see the new results.