Okay, I've released a new build with a menu option for this:
Let me know if that doesn't work with any mods you're using.
That was quick! And it does seem to work, at least with Netronian Chaos... although I have to launch GZDoom without it first so I can adjust the setting, as it does not appear while Netronian Chaos is running. I guess it is not your fault that the mod's options override yours.
What I do not understand with the reset inventory is that it makes most secrets pointless, since they do not carry over to the next level. This is not your fault either, just something that strikes me as odd with the Master Levels' original structure.
In any case, thanks for the update and for the compilation! :D