They are not rated seperately. People will vote based on the aesthetics of the map, and rank them against each other regardless of if they're a spawn room or intel room.
The intent was to give people two options for what they could do, to be less restrictive. The idea behind allowing people to merge them, was rewarding the extra effort (you're essentially doing two entries work for a single entry) with the much larger size limit to encourage ideas.
If you do both in one entry, it will still count as one entry and you won't get bonus points for it, but you will have four times the space of other entries to impress people.