I tried removing the Snake and then the add-on manager to verify if it was either of those but the FS still CTD if I exited from the Flight directly; So, I thought it was something else within the game. I uninstalled KJFK entirely and the CTD went away. Then I re-installed it and the CTD came back even if the snake and AM are disabled in the dll.xml/exe.xml files.
From your description, it seems that the CTD is not caused by the Addon Manager or Couatl. BUT, Couatl itself is not able to close down if FSX doesn't close cleanly. Which is something we might be able to fix, but it certainly wouldn't fix your issue entirely, except for not having to manually close it down from the Task Manager anymore (in case FSX crashes)
So, it might look like as if the *scenery* itself is causing the crash, rather than the two executable modules.
However, as we have seen in other cases as well, more than the scenery, it might be something that appears only when the scenery is installed, even if it's not part of the scenery per se. For example, by installing JFK, the very presence of its AFCAD file might attract a much bigger quantity (and different models too) of AI, comparing to the default. And, one of them might have a problem which causes the crash.
The only thing that's sure, following your report, is that neither the Addon Manager or the Couatl module are causing the crash, because you are having it even with both disabled.