Yes, Unicode 6.0 only has 7
Latin ligatures - ff, fi, fl, ffi, ffl, ft, and st. So I guess any others would have to go to a private area.
One would hope that ADE and the RM implementations would be smart enough to check the current font for glyphs, but maybe they hard coded some range checks instead. Have you tried the Firefox epub extension or any webKit implementations?
You could zip your file - that should be accepted.