As I’m sitting here in the cathedral, it wouldn’t be hard to make 2nd level and 1st level shops with all the gates going to the outside… I guess it depends on shop size, etc… but this goes back to whether you are looking at individual shops given a certain ground space (10 x 10?) or building a structure like a cathedral and having 10×10 spaces for rent?
I still like the general layout of the Pentagon, 5 sided and provides the shortest walking distance if spawn was set in the center. From Wikipedia: It is possible for a person to walk between any two points in the Pentagon in less than seven minutes.
Now Minecraft doesn’t do anything but square good, but I’d still focus on a ring layout with the spawn in center. Thinking of the Cathedral, spawn could be right where the flower design is in the middle of the floor. Just some ideas…