I mean, all Guardians have control over Chaos energy, like Knuckles’s father Locke. Knuckles’s abilities like Flight come from manipulating Chaos energy, but I think things like flight are passive controlled. Passive, I mean, I don’t think when Knuckles uses flight, he is aware he is using the Chaos Force. At least in the beginning.
Also, in a more obvious moment of Base Knuckles Manipulating the Chaos Force, was in Sonic Universe when he and Dr. Finitevus tangled. Dr. Finitevus was shown to use the power of the Master Emerald before in his benefit and Knuckles matched him.
I’d imagine Knuckles hurting Bill a lot with just his fists. Base Archie Knuckles almost broke through a de-powered Egg Wily Machine X, and i’m sure the de-powered EWMX is more durable than the Mystery Shack that Bill fought.
It's not a stomp. Again, I don't agree with it, but the rules are that if two characters can win, but one is simply always faster it's still not a stomp. If transmutation was passive then yeah sure it's a stomp but Knuckles technically has a chance to win so it's not a stomp
Again I don't agree with it, but those are the rules
This is of course assuming Knuckles has take down Bill theoretically