None of these things are “divergences” from the MCU, and a particular story doesn’t mean “non-canon”.
The show simply didn’t mention the snap/blip, but not mentioning something isn’t proof that it didn’t happen. The framework was computer simulation, I have no idea why that would be proof that the show diverged from the MCU. And just because the movies didn’t acknowledge stuff like Coulson’s return or the Inhumans doesn’t prove their non-canon status, nor do they have any crossovers yet in the latter stuff. Maybe one day wonder might decide to confirm them with a crossover, or maybe not, but the only thing that would make the show “non-canon” is if they introduced elements or characters from the show in a way that clearly makes the show impossible