Of course, mods don’t rely on official DOOM assets to function, only on its source code which is public domain, so using FreeDOOM to play these mods for free is perfectly legal.
However, having just tried that myself, I realized some custom sprites just don’t mix well with FreeDOOM. The artificer’s pistol’s secondary attack, which cuts enemies in half, relies on custom sprites that were created specifically for the monsters from DOOM and DOOM II (as well as the custom monsters from Malefactors), meaning that the monsters from FreeDOOM will suddenly turn into those from the official DOOM.