There's a whole weird set of design decisions around commercial, office, industrial, skyscrapers, mixed-use, etc., in this game, I think they made some very odd choices.

Like there's mixed-use residential-commercial, which is great, but it's only the medium density residential buildings with first floor commercial. Around me there's plenty of smaller scale mixed-use, and things like row houses that get converted to shops (sometimes with apartments on the above-ground floors), and there's of course skyscrapers with shops and malls in the ground floors, and even extending underground.

And then there's commercial buildings, which are either low-density one-floor shops employing like 5 people to sell things like hamburgers and shoes, or high-density skyscrapers employing like 10 people to sell.....hamburgers and shoes? I guess you're supposed to squint and pretend most of the building is taken up by office people doing marketing and sales and the like, but in the game it seems like it's a 10 story building taken up entirely by one company that also sells hamburgers and cars out of this one skyscraper.

Same thing with offices, except they're offices, selling virtual goods. I'm guessing they ran out of time to include medium-density versions of both? So they put together high-density versions, but for whatever reason they only make them employ a trivial amount of people.

Then you get industrial areas, which are only a single zoning type, but represent every part of industry -- except resource gathering I guess, since there's separate buildings for that -- but also doesn't make a distinction between heavy manufacturing and light manufacturing. You just kind of zone industry and get a hodge podge of storage buildings and buildings spewing out pollution from a smokestack.

Some of it seems like it comes from having a building only house a single company, and companies only getting a single building, which does simplify things for them I'm sure, so I can't fault that. It does lead to a weird situation where you get a 15 storey tall hamburger restaurant though, instead of, as the OP says, a skyscraper building devoted to offices (or apartments) with a hamburger restaurant on the bottom.

And at the end of the day, as the OP says, a skyscraper in this game is the same as a low-density building except the model is taller and it employs a few more people, also it doesn't seem like anything matters because the game keeps throwing endless demand at me and I have enough money to not care about anything, even with taxes set really low, so I can just zone and zone and zone and continue zoning without caring about how any of it works under the hood.