ZDoom

I was just wondering if there is any way to tell GZDoom not to look at my GOG installed games (Steam too, I guess, but that's irrelevant to me).

What I want to avoid is GZDoom popping up the IWAD choice dialogue with IWADs that are not in the folder that GZDoom was started from. Currently, with a particular install of mine, if I double click GZDoom, I get a list of (custom) IWADs in the same directory as the EXE but Strife and Strife VE are also listed. These are not in the directory (they are installed via GOG) and I don't want them to be listed as an option in the startup dialogue.

Not a major problem but, is it possible?

This really needs to be settable in a way that custom games do not get hijacked by these IWADS, but I do not have a good idea how to do it,

Most custom games are going to need to ship a custom gzdoom.ini anyhow, in order to set default keybindings and visual settings that are recommended for that specific game.

A CVAR would be the best way to do this, I think.

Not for keybindings. Those can and should be set via the defbinds lump.
Regarding custom INIs, so far the first thing I did with those was always to delete them because 99% of them screw everything up for me.