The Jury is not out. The verdict is in. Ford engineers put the 1 bolt on all 2.3L Explorers and the 2 bolt in 3.0L Explorers and Aviators in MY2020, and at least early MY2021. I'm sure there is good reason for that. Supporting that, the OP got a two bolt subframe as the repair for his MY2021.
The jury may be out on why later build 2021 3.0L have the 1 bolt, but that is not the way they were originally engineered. If I got the one bolt, I'd be pissed. Would it change how I drove it? Not while under warranty. I'd drive the snot out of it (untuned) and see if the rear setup could handle it. If they start getting a bunch of these failures, they may indeed be checking for aftermarket tunes, if only to limit the liability.