Just updating this thread on the outcome. The SuperATV flip windshield and the OEM Honda roof both fit on together perfectly without anything needing to be changed (2022 Honda 1000-5 Trail). I put the windshield on first and then the roof. The front roof clamps were a bit a of a squeeze, but just took an extra couple minutes to navigate/clamp down it all.
Definitely recommend using Loctite on the bolts used for the SATV windshield that do not have a locking nut on the back (first ride out and one bolt fell out/was lost and another was coming loose). As others have mentioned, don't get Loctite on the plexiglass...they don't mix (will cause cracking/brittleness).