I personally have never baked a ‘lightmap’ before. Maybe that’s due to less experience with games for me, more experience with offline rendering.
But I think the answer is yes. For objects to share UV’s they need to be identical meshes. So let’s say you duplicated a crate a bunch of times in a game level. Each crate could share the same UV’s for the crate texture but each would need a unique secondary UV map for its custom lighting info to be baked to. You should be able to simply add a new UV map per duplicated crate and bake individual maps to that second UV map.
