As far as I know nothing gets changed in the FSX.cfg when you install a FSDT product, except that in the Trusted section you will have two enteries like this after your initial install and you approve those two modules.
[Trusted]
C:\Program Files\Microsoft Games\Microsoft Flight Simulator X\bglmanx.dll.kunuaknlnnzeliarkniwwweoetuhcrrqzlhabwze=1
C:\Program Files\Microsoft Games\Microsoft Flight Simulator X\fsdreamteam\couatl\couatl.exe.atznhhqouowwnwztwqcqtwqkkbwqhrzerwnwloek=1
Aside from that the only way to change FSX.cfg settings are if you change and apply them using Addon Manager. If you didn't do that then nothing else should be changed just by installing the product, aside from what I mentioned above.
In fact, I always make a back up of my fsx.cfg, scenery.cfg, exe.xml, and dll.xml before I install anything new. In the past after installing a new FSDT scenery I see no changed to it, or in FSX performance for that matter. Perhaps its just a fluke that your performance seems different, or you changed something else somewhere along the lines and forgot.