I believe it has something to do with mobi itself, which declares that author is LN, FN and refuses to acknowledge any other possibilities. So any other program reading mobi and asking for author's names gets it in the order mobi has them in its metadata - LN,FN. And as it will not be proper mobi if the names are swapped around, the mobi-making programs won't even dream of it.
I don't think it's possible to tell Calibre to swap only authors from mobi/azw files and let the others be.
I have to edit the metadata after adding a book anyway, and once in a while make search for authors with commas.
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