The rules are provided as a way to price buildings. Each building is made of rooms, so if you want the building you just sum up the room's value and get the total result.
In real life you don't build the rooms separate from each other because that would mean building a lot more walls, all the walls need to be load-bearing, residential zoning is subject to taxes and you try to build rooms adjacent to one other and on multiple stories.
When you build on multiple floors, you also want your base floor to be quite large.
When following these oversimplified rules those issues don't come into play (literally).
Building a room with load-bearing walls, a room with simple walls or a room that is enclosed by the walls of other rooms costs exactly the same, there are large lots of land you can buy in most fantasy towns and you don't usually get taxed for owning them or need to spend a lot to buy a lot (sorry for the pun). You don't make stability assessment either.
In a world like that, everyone builds separated rooms because it's convenient, unless you want to enforce some sort of realism and tell your players "let's say you can have a separate lab or store but your house has to be built all in one piece, please".
Or, you know, I'd pay a little extra for having the bathroom inside my house, rather than 35' across the lot, especially in a rainy day.