In the former case, they filmed jets and jet cockpits, but all of the jets and cockpits are replaced by CG ones, only the actors remain if they are visible.
In the latter, in the motorcycle chase scene and when Tom jumps over the edge, aside from him and the bike, basically everything else is digital, e.g. digital train, terrain, trees, ground and everything.
They jumped the train off a bridge FOR REAL at the end of the chase, but then paint it over completely with a digital train. The only thing that stayed is some water splashes, that’s it.
This is intentionally concealed by the studio marketing saying it “was practical”. Yes they did do it “for real”, but it erases the work done on all of the digital effects that end up making up the majority of what you see in the movie.
That’s just dishonest, and what people are upset about.