Among many other things, like the Clone Saga clones having his powers, a Sentinel straight up scans Peter Parker and mistakes him for a mutant because his DNA has literal spider genes in it now. That's just Spidey canon.

Same with Super-soldier Serum that gave Rogers his power, it was a genetic modification and, eventually, the same is true of Weapon VI aka Luke Cage (Weapons Plus being a descendant program, he received a modified version of the Serum)

In Marvel comics there's generally a distinction between "mutants" and "mutates." A mutant got their powers from birth, typically from the X-gene, a mutate had something happen to them, but that's not a real scientific distinction. They've all been mutated. It's just in-universe discrimination and is often specifically portrayed as such. Like all discrimination, the distinction is quite often arbitrary and unjustified.