I agree with you about that statement, but why don’t you commit to an unstable branch? Why risk losing something or pass up having a better development history?
The way the warning is worded suggests that any invocation of tup has a risk of deleting your files, implying that to be entirely safe you should commit before every single build, which would be ludicrous.
git commit --amend, rebase with squash/fixup, etc. I easily make a dozen commits per hour, it's like undo on steroids and you can always clean it up later.