Apologies, my first post might have created some confusion.
After browsing MakeMusic and skimming through the posted p001.xhtml, I realized that the EPUB3 exported by MakeMusic does not seem to have audio (hence, no media overlays/SMIL), but it contains only the score, in SVG format.
So, to eliminate OP's first post errors, it suffices to remove the
Code:
media-overlay="..."
properties from the manifest items.
Hitch, to answer your question: with no SMIL files no synchronous highlighting is possible (not only in iBooks, but in EPUB 3 in general). Moreover, since Media Overlay is not part of EPUB 2, such a functionality is not available in EPUB 2.