I do this all the time in almost any repo I work in. I usually just keep the difference as “junk” in my local work tree.

I never git commit -a anyway, my commits are always kinda prepared and meticulous.

I just live with the spurious diff and extra stashing. All alternatives seem to complicated. I do love the way Jetbrains IDEs manage changesets though. It is a big improvement over only (not) using git for this, but I rarely use their IDEs nowadays.