Are you allowed to score in the middle row of goals during autos

Exactly as the title says, are you allowed to score in there without DQing yourself from autos?

Yes. Mainly just don’t touch the tiles or push balls to the other side that would affect there auton

And you wouldn’t get dqed if you went to the other side or messed up their auton. They would just automatically win auton

Any question that asks “are you allowed” or “is it legal” should be answered by consulting the game manual. In this case the relevant rule is <SG2>:

(emphasis mine)

…unless you violate the rule in an “intentional, strategic, or egregious” manner per <SG2>, which would result in a DQ.