I highly doubt merging multiple level mods would work though even if mods are capable of modifying the main campaign maps.
Still, that would be enough for people to make mods that alter the main campaign without having to restart. You may only be able to have 1 active, but it's better than nothing in my opinion.
So my quick attempt to modify Cyseal both before and during a game failed to work (copying and modifying the Cyseal level in the Data/Mods/Mod_Name/Levels/Cyseal/); the rocks and Rain scroll that I deleted in the Editor showed up when I loaded the game.
Mid-campaign, this kind of makes sense; the map changes immensely during the course of the game, so changes to the base map won't have any effect.
It not working pre-campaign however points to it either not working or me not doing something correctly (both of which are highly likely).
