Those are all intentional. The entire bowling alley is all loaded, but the thing is, the middle wall is random, and both of the walls are paper thin. You wouldn't be able to see them in top-down view, and they'd obscure each other in side view. I chopped out the back portions to only show what it looks like most of the time. The Bombchu Market isn't there because, well, I can't figure out how to get it open. I tried using cheats to get quest items and go places, but the Shop Owner and the Bombchus haven't appeared yet. Without the owner, the collision model of the shop is pointless. I'm going to update the map as soon as I can find the guy. I'll just have to play it normally until the guy appears. As for the treasure box shop, I wasn't sure what to do. If I remember correctly, it will take up a lot of room, and mapping it would require me to actually win the shop game. I'll think about it. If anything, I'll still rip the rooms to show you.
I'd also like to mention that I left out characters in the main Market square who always move around, as well as Malon, since she's only there the first time.