You can stack 2 “different” UV maps on top of each other and not have them interfere because they are using different texture.
Let’s say you UV map an arm and leg separately, give them separate textures. You can merge them, merge the UV channel, have them overlapping, but assign them different materials and it’ll work perfectly well. (Or you can offset one of the models UVs by 1 so they aren’t visually overlapping, but effectively does the same thing).