I wouldn't pretend to know what might happen to one of these experimental hybrids(?) if submitted to KDP. I can only say that I, myself, would never recommend doing such a thing. I think the idea behind this (and the more basic "splitter" functionality of Mobi_Unpack) was to give options to those who might be planning to distribute their own files/books. Or for other, similar personal uses.
Unless it's a standard old-style, plain-jane mobi or the new "official" combo mobi/KF8, I don't think I would consider submitting it to KDP.
Just my opinion of course... other's may vary.