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.
It’s worth noting that mutants are often the ones making distinctions, even the X-Men…
If you’re born with powers but don’t carry the x-gene they’ll be the first ones to tell you you can’t be in their club, even if you used to be in it when they thought you carried it (see Wanda and Pietro Maximoff or Franklin Richards for notorious examples).
