The .garbage file does nothing to address the fact that if you open a non-well formed EPUB created outside of Sigil (for example you want to fix the file) auto cleaning can potentially cause content to be lost.
Fixing the root cause of the issue that content can be lost is where the focus should be. A .garbage file only works around one possibile situation and doesn't actually solve the issue.
There are only two ways to solve this issue. 1) don't use autoclean because it's un-reliable. 2) Don't autoclean non-well formed files.
I don't like option 2 because you can still have data loss with well-formed content. Which is why I don't like or recommend using Tidy.
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