Sceneries for MSFS and P3D cannot possibly affect each other so, in case of Basel, just install it in MSFS with the FSDT Universal Installer, which will allow you to do that, since it will see the license is active for P3D.
There are no issues with using GSX and GSX Pro, they are designed to run together.
However, they DO share most of their code so, it might be possible something P3D-specific might not work perfectly, but that's why there's a P3D support forum for so, if you find any issues, please report them there.
