Generally, you are right. It’s better to have lower consistent framerates than higher framerates with frametimes all over the place. That creates microstutters that are extremely displeasing.
However, if I start at an airport with 30-35 fps and return to that airport after an hour of flying, I expect to get 30-35fps again not 12 or 14. That’s the issue. The Minupulators take 15ms instead of 3ms which slows down the main thread and makes the whole simulation CPU-bound where it wasn’t before. That’s a bug and nothing else. And there’s nothing in the settings that can optimize or compensate for that. That’s simply a bug in the engine with (supposedly) garbage collection not working and slowing down a process with lots of data which is not thrown out when not used anymore.
I get your whole point about frametime consistency and I agree. But the framerate should be the same after an hour of flying and returning to the same airport again. And the manipulators should take the same time to calculate.
Off topic: I was on board since the MS-DOS launch of Flight SImulator II in 1984. 
The more I think about it, my issue might be related to After playing a few hours, FPS drops from 40 to 5FPS