This is the way I do it as well.
I created a fake FSX installation with the path "C:\Program Files (x86)\Microsoft Games\Microsoft Flight Simulator X".
Within that, I added the Addon Modules, Addon Scenery, Effects, Gauges, Modules, Scenery (including the World\Scenery sub folders), Sound, SimObjects (including the Airplanes, Animals, Boats, Rotorcraft, GroundVehicles and Misc folders) and Texture folders.
This way, whenever I have to run an "FSX only" installer, I just point it to this fake installation and let it run.
Then I just check each folder and if something was installed to it, I just move it over to the similarly named folder in my P3Dv4 installation.
It sort of seems complicated at first glance, but it's actually pretty easy to follow, once you do it the first time.
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