If I understand your project correctly, perhaps you can use audacity’s macro feature to help. I tried the following with Audacity on Windows:
SelectAll:
Copy:
Import2:Filename="c:\\users\\jademan\\Desktop\\SilenceA.wav"
SelectTracks:Mode="Set" Track="2"
Paste:
SelTrackStartToEnd:
ChangeTempo:Percentage="-66.667" SBSMS="0"
Import2:Filename="c:\\users\\jademan\\Desktop\\SilenceB.wav"
SelectTracks:Mode="Set" Track="4"
Paste:
Import2:Filename="c:\\users\\jademan\\Desktop\\SilenceB.wav"
SelectTracks:Mode="Set" Track="6"
Paste:
SelectAll:
Align_EndToEnd:
ExportWav:
I think it may do something similar to what you are looking for. You may wish to review the following links:
https://manual.audacityteam.org/man/manage_macros.html
https://manual.audacityteam.org/man/macros_examples.html
Create your two SilenceX files, install the above code as a macro, load in your first clip, and apply the macroo the Project. If you are happy with what you see, Apply macro to selected files. Results to to macro-output subdirectory. Then all you have to do is merge all the files in the new sub-directory.
I hope this helps.