https://wiki.mobileread.com/wiki/EPubHacks also contains some suggestions about small caps.
Seems to me though as if there just isn't a good solution.
My current calibre settings would filter your smallcaps hack right out. There are too many books with whacky font sizes defined in them - on Smashwords probably because they use Word/DOC as a source? - so font size is one of the properties I filter out when converfixing books.