The answer is, neither of those latter two things ever happened, thanks to Days of Future Past removing those two movies from the continuity.
One of the major plot elements in Days of Future Past is that Wolverine changed the timeline, thus altering everything that happened from 1973 forward. The produces of the X-Men series have openly admitted this, both in-universe and out-of-universe.
Specifically, Days of Future Past completely nullified the events of X-Men Origins: Wolverine and X-Men 3: The Last Stand. Anything you saw happen in those two movies, you can pretend did not happen.
The two scenes you cited are, in fact, two of the scenes we know for a fact cannot possibly have happened.
We know from X-Men: Apocalypse that Jean came to Xavier's school as a much younger woman, seemingly of her own accord, and that Magneto was nowhere to be found when that happened. There also does not appear to be any "block" on her psychic power. So, there's no way that Xavier and Magneto went to her house together to meet her as seen in X-Men 3.
We also saw Stryker's facility where Wolverine was being kept, and there's no indication that he was holding any children hostage. Xavier's school was already well established by the time Wolverine escaped from Stryker, and the entire ending scene (breaking the children out, fighting fake-Deadpool, etc) just never happened.