Yes, most do, although more recent installers will use an alternative if it is available.
Some installers add effects, and there is still the need sometimes for elevation stubs in Scenery\World\Scenery. The main Texture folder normally includes custom autogen textures -- these are blgdz2 textures for local housing, and will be identified by 'GZ' in the filename. Haven't found an alternative location for these, yet, maybe with P3D v4.
The older stuff (which is anything prior to Real NZ Nelson/Subscription) is a bit of a lottery, as none of these have P3D3 installers.
And of course the default location for FTX stuff is still the same, so any FTX files edited by my installers would be with the P3D folder system.
Oops, forgot about VLC.
Yes, VLC changes a lot of default files, from memory.