Yeah, I've also heard about this 'incompatibility' issue, which to be honest, I can't help but feel is complete nonsense especially in this day and age ......unless it was literally recorded on the U.S.S. Cygnus!
The iTunes version is a disgrace and certainly doesn't sound as good as the 'Mask boot', this score deserves much better treatment.
Hopefully in the not too distant future, one of the specialist labels will be in a position to do something about it.
The total running time of the missing cues isn't that much but I really feel they would help to flesh out the score and to break up a little of the repetitiveness.
Anyway, fingers crossed!