No, they coexists, because the actual code *is* mostly the same, and the things that are different ( graphic models ) are invisible to each other.
Airport profiles are surely separate for MSFS, since they are in %APPDATA%\Virtuali\GSX\MSFS
Aircraft profiles are in the same folder, but it's quite uncommon to have an airplane with the same name in MFSF and P3D and those that do, it's because are dimensionally equivalentnt.
Setting are shared, we are a bit torn about this, some users might find nice their preference to be shared between P3D and MSFS, others might prefer separate.