Were Lindzen and Choi treated differently by PNAS when submitting their latest study?

Can't judge the specific technicalities, but the conclusion of the question seems unlikely at best. Lindzen has an extensive roster of peer-reviewed publications. They offer little backing for his periodic public statements indirectly supporting anti-science denial, but that is his personal ethics issue; the publications are judged on their merits and usually get published. It happens sometimes in science that people think just because they are senior practitioners that they can get anything published they want to. Sometime they get away with putting out substandard stuff, sometimes not. Whether something like that is going on here is unclear, but I doubt that there is any "game changing paper" involved.