I'm sorry but I just cannot buy much of that old concept art. Looking at the video for Japan's World, the land is U-Shaped. The tallest portion - the one with the coins that Mario climbs - doesn't appear to have anything of interest in it, so it seems to be nothing more than camouflage to hide the blockiness of the ride building, as well as all the rooftop equipment that sits on these ride buildings. So that ride building apparently runs the length of the land from Bowser's castle to the coin tower. The only other area that seems to be camouflaging roof equipment is the area to the left of Peach's castle, so I'm calling this a ride building also. Whether it stretches all the way to the corner or not is harder to figure out, but the plethora of doors in the corner between the two castles suggests food and restrooms, so the ride building probably ends before the corner (that one second-floor entrance looks suspiciously like a slot machine, which suggests an arcade). This is only THREE buildings: one long ride building, one shorter ride building and a building for food between them. And, yes, the buildings WILL be separate, regardless of how they connect them on that second floor. Food buildings require way more infrastructure than ride buildings, so the two types won't be combined.
I can't see fitting more than one ride into either of these buildings. Mario Kart will need tons of space and the other is only about as big as ET, I guess. And I don't see them altering too much of this as it moves to the other parks, and we know Universal likes to change as little as possible when cloning. This plan plops down almost perfectly into USH's Lower Lot between Transformers and The Mummy. The pipe entrance would just have to be moved and Mario Kart would go into the Mummy building, so they'd really only have to move the entrance to the ride and shift the coin tower and Bowser's castle, all of which would be simple enough to do.
As for USF, even less would have to happen. It could built exactly the same, without even needing to remove the Animal Actors or ET. Even better, there looks to be room to build out the front, so they could probably repurpose the coaster and Fievel's Playland, which could both remain running until after the land opens, which Universal desperately needs to do. Adding in a flat ride or water play area would be a piece of cake.
I also don't see either of the 2nd-level castles being the entrance for rides. Peach's castle is super-skinny, little more than a facade. Maybe it'll be a meet-n-greet or a small princess shop. Bowser's castle definitely looks more like a proper entrance, but I can't see how you'd put a queue on top of a ride building. That jacks up the cost right there. Plus, the mushroom on the bottom floor just seems like a better themed entrance. This is a Mario ride after all, not a Bowser ride. It also just makes more sense for people to have easy access to rides. Everything here is stairs, stairs, stairs, and I don't see Universal expecting people to climb them or go up elevators/escalators, to get to rides. I don't know what else Bowser's castle would be for, but maybe a gift shop exit? My problem with a two-story land is that many people might just look up at the second story, see all the stairs, and just say to heck with that. Letting them enter on the ground floor but having them exit right in the middle of these shops makes a ton of sense. People didn't have to climb stairs to get up there and they only have to go down them on the way out!
As for the missing stuff? I think it's very telling that they named the land "Super NINTENDO World" when it looks like it's 100% Mario. (And the Super Nintendo console was how many years ago?) That tells me that expansions are definitely on the way. Japan has space to expand near the entrance, Hollywood appears to be making room in two separate areas for expansions, and Orlando can retheme Toon Lagoon or Lost Continent AND build a whole new land in the new park. It would then be easy to rename the original land "Nintendo's Super Mario World" (which makes more sense) and have future lands be "Nintendo's Donkey Kong Country" or "Nintendo's Dream Land" (though if they repurpose the coaster and play area in USF, Kirby seems like the best theme) or "Nintendo's Land of Hyrule" (I don't care how universally popular the Zelda characters are, that franchise will allow for some spectacular theming and ride ideas). So, by calling this Super NINTENDO World for now allows the other Nintendo characters to roam about until they get their own lands!
My two cents.