For most Marvel characters coming out of the SECRET WARS event, nothing during the event is relevant after it. There are multiple versions of most of the characters, and nothing that happens to them carries forward when we return to normal.
The exceptions are the handful of characters who haven't returned to "reality" yet, and the characters who came from different Earths. The first group is primarily the Richards family (they'll be back eventually, FANTASTIC FOUR can't stay gone forever). The second group includes Old Man Logan, Miles Morales, and Red Wolf.
I believe Ms Marvel makes appearances in INHUMANS: ATTILAN RISING and A-FORCE (and maybe in SECRET WARS: SECRET LOVE - I didn't get that one), but she wasn't a major character, and nothing there is relevant to your v 5 trade.
As you noted, coming back, she has become a member of
The (All-New, All-Different) Avengers.
Basically, post-Secret-Wars, all the books picked up several (8, I think) months after where they'd left off. From what I've read since, only major events from that time period will be revealed. Thus far (to the best of my knowledge), the only event that has been revealed is the discovery of the impact of terrigen mists on the mutant population (in DEATH OF X).
Unlike when DC did something similar years ago ("One Year Later", after INFINITE CRISIS), there has been no announcement of a series (like DC's 52) to cover what happened during these "missing" months.
In this case, I suspect Marvel mostly wanted to avoid the confusion of dealing with what people did or didn't remember out of SECRET WARS, especially when the time came to deal with those characters who did get moved into the "regular" Marvel U. It seems logical that, if anything else of real significance happened, it will eventually be dealt with. Otherwise, we should assume that things happened in an unremarkable way. As with that other book: Ms. M (and the other two youngsters affected) had existing connections that could logically lead to an invitation to join up and be trained, without the need for some unknown major storyline to bring it about.