This is just my approach to big franchises in general. Once a franchise gets to a certain size there's usually expanded media that mostly go ignored by the main installments (think novels, comics, audio dramas, etc. that expand on a tv show or movie series), as well as installments we'd all like to forget (terrible sequels that retroactively ruin what came before or what have you). So at that point it's best imo to just pick and choose whatever bits you like.
For me that means that some version of most of the shows still happened for the most part until they're directly contradicted. But when inevitably a different version of some character that was on a show shows up it won't bother me.
Since this thread is active again, I'll point out that besides Gemma Chan there was also Kenneth Choi playing his own descendant and Michelle Yeoh playing two totally unrelated characters. As well as of course Cumberbatch being both Strange and Dormammu in the same movie.
It hasn't happened as much so far, but this stuff happens all the time in long running tv shows. And it will probably happen again in the MCU. I don't think Marvel will exclude the likes of Kate Mara, Olivia Munn, Justin Theroux, David Bradley, Richard Armitage, Jenna Coleman, Natalie Dormer, Jenna Ortega, Tony Curran, Adewale Akinuoye-Agbaje, Talulah Riley, Danny Pudi, Nathan Fillion, Seth Green, Julian Bleach, Clancy Brown, Matt Damon, Sam Neill, Luke Hemsworth, Ving Rhames, Miley Cyrus, Carrie Coon, Ken Jeong, Yvette Nicole Brown, Melissa McCarthy, etc. from future casting. Nor do I think Josh Brolin having been Thanos will prevent him from returning in Deadpool 3 as Cable.