Ford knows exactly what part number they put in your car. In all these cases, the 3.0L powertrains specifies the two bolt. I don't know who made the call but in all likelihood some 50k+ Explorers built in 2021 were made with one bolt subframes when the two bolt is specified. I would definitely call Ford's customer service line. The dealer may tell you they can't do anything if something isnt broken. To me, it's more you are missing something that should be there. If possible, crawl under there and capture a pic of the subframe part#. For sure that will not be the same as what's specified for your model.
Definitely if your differential is not sitting even, that shouldn't be. Maybe your front mounts are wonky too or maybe that bolt is already damaged but that could start the discussion with your dealer that you have the 2.3L subframe and it should be the 3.0L. If enough of you contact Ford and hopefully those with broken single bolts have reported this with the NHTSA, maybe you can get a recall issued. It may not fail during warranty period but if it does after, it's a high dollar repair. One guy reported that the dealer fixed his one bolt and then a short time later, it failed again!