I have this same issue with our Watch app schemes and have also submitted a feedback request (FB9832417) the resolution status has been updated to "Potential fix identified - For a future OS update" so hopefully we'll have a fix soon.
Removing it from the repo doesn't work for us since it results in that scheme not showing up in the schemes drop-down. Using git update-index --skip-worktree
doesn't work well on a large team since if everyone doesn't do it then it causes issues, and the docs for that command warn that it isn't meant for this type of use case.
My latest workaround is to add a pre-commit hook that discards the changes to those scheme files before committing so that it doesn't show up in our pull requests at least. Still shows up in the local diff before committing which is annoying but it's the best i've been able to work out so far that doesn't depend on everyone aligning on the same behavior.