Okay, so here’s my unconventional solution to my unconventional problem:
I made symlinks in the Content/__ExteralActors__ and Content/__ExteralObjects__ folders that point to [MySubmoduleFolder]/.ExternalAssets/Actors and [MySubmoduleFolder]/.ExternalAssets/Objects.
Git seems to handle the symlinks just fine as long as core.symlinks = true in the git config.
The parent repo needs to be updated once to contain those symlinks, and can then be left alone.
UE accesses the files through the symlink as if the files were in the expected location and I properly get the file changes to my submodule’s file change list. The .ExternalAssets folder name causes the UE Content Broswer to ignore that folder, also avoiding potential problems there.