In my experience, CX can show different class/bucket availability depending on whether it's a through ticket or a single flight. For example, individual JFK-HKG and HKG-KTM flights might show I availability while JFK-HKG-KTM might not (or vice-versa), even if they're the exact same flights. And even if you have a stopover in HKG.

Also, in the case of CX, availability on ExpertFlyer doesn't always match up with actual availability when booking. I've found that if ExpertFlyer sees I, it is an indication that the fare may be bookable, but not a guarantee.

Regarding the availability being different for new tickets vs. changes, that seems a little unfair. But nothing is surprising when it comes to the mysterious and opaque world of fare availability...