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The remove formatting action is not implemented at the level of calibre code, and as such I have relatively little control over it. In the next release, I will have it automatically do the switch to html and switch back roundtrip after a remove format which should address some of your problems. The rest you will have to live with.
Also, for me, remove format not removing headings and other "structural markup" is a good thing. I expect it to only remove inline style bold/italics/color that sort of thing, not change hte structure of the document.
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