I haven't seen any issues between UT2 and any of our products, including JFK. They just work, as the below screenshot shows.
The only thing to note, is that UT2 traffic takes a little while to appear after the scenery is loaded, but that's entirely depending how UT2 works, by injecting traffic using Simconnect instead of a .bgl, but this happens regardless of the scenery, it doesn't have anything to do with the Addon Manager or the trial version but, more probably, because generating traffic in the JFK area takes a lot to compute all the flight paths, since it's a very busy area.
While I am at it, I was also wondering about a few of the terminal buildings and jetways that seem to be floating on one side of the airport. but I chocked it up to trail mode that was causing that as well.
Please, be more specific, and list exactly which buildings and which jetways, so we can check if it's really a problem of the scenery, or it's something else on your system that is affecting it.
Of course, it doesn't have anything to do with the scenery being in Trial, as we said many times already, the Trial is EXACTLY like the full version, just it runs for 5-6 minutes at a time, but there aren't any other limitations and it's not crippled in any way so, if you find somethign that doesn't look right, either it's a bug of the scenery that will not go away when purchased or (most likely) it's something else in conflict.