You're absolutely right.
I never notice the issue before. It appears that 7-zip (at least this
version of it) is rearranging the archive a bit rather than just adding the file.
The Tweak Book feature of calibre would be my suggestion in that case. No conversion necessary to do that. 1) Explode the ePub. 2) copy the the xml file to META-INF. 3) Rebuild the book.
I just verified that the above process keeps Epubcheck happy. It's unfortunate that there's not a less convoluted way for adding this file to ePubs--for users on platforms other than OS X, that is. The situation seems ripe for a "tool/addon."