Quinn hinted to Tuvok that the Q may use some type of really advanced technology to do what they do.
That suggests some type of limitation.
"You and your ship seem incredibly powerful to lifeforms without your technical expertise. It's no different with us. We may appear omnipotent to you, but believe me, we're not. "
This is more about perspective of ability, not the manner in which those abilities are achieved. The Q can will a bronze sword into existence, and human's can create one as well, but this doesn't imply the Q need to forge one from scratch, nor can a human 'think' one into existence.
With Quinn, he is more apt to using an abstract, philosophical perspective to undermine the defining quality of being 'omnipotent', which is in and of itself, a paradox:
Can an omnipotent being create a stone so heavy that it cannot lift it?
If yes: the being has a weakness (being unable to lift the stone) and his power is limited, or becomes limited.
If no: the being's power is already limited, since there is an action he cannot perform.
Either way, the allegedly omnipotent being has proven not to be omnipotent due to the logical contradiction present in both possible answers.
The bottom line is, yes - the Q, - by the writers submission of material - have unlimited control of space, time, and matter, as well as can be defined and presented in a manner which satisfies their story; They do not, for instance, create comic book demonstrations like blowing up entire galaxies.