Again, it all depends a massive amount on the individual house. Yes, there are houses with rooms of the same type grouped together, and there are also plenty of houses where the types of rooms are somewhat randomly distributed, depending entirely on the people who live there.
As for pipes, again not really. You're much more likely to find rooms requiring water pipes have a shared wall and / or are right above each other. A second floor bathroom is more likely to be above the first floor bathroom or kitchen, since then you have less pipe to run around and some types of pipe require a thicker wall. Similarly a bathroom is more likely to share a wall with a kitchen than not, again due to needing to run less pipe around.
Regardless, I'm going to leave this here to not continue off topic.
While you are correct about plumbing for upstairs and downstairs, in some cases, You're being too pedantic about specific house types. I'm just speaking generally. Not allowing for renovations, specific setups and the likes, it's about the flow and location of rooms. My argument is about UI layout, not what houses you've seen in your life.
Right now, it goes Entry > Sam's bedroom > Kitchen > Bathroom > Living room > Robin's room. Most of the activities happen in the living room and kitchen. It would be more natural to go Entry > living room > kitchen > Bathroom > Bedrooms.
The reason for his is that the living room should be the common room, right after the entry, the bathroom is often something you do before bed, or after waking up, so should be next to the bedrooms. Then, after you've cleaned up, you can either go to the kitchen or bedroom, depending on time of day. Then in the mornings before school, you meet Robin in the living room, before exiting, which makes sense to leave from the living room at the front of the apartment closest to the door.
The UI button issue is more than the apartment, it applies to other areas too, such as the apartment courtyard. You exit to the courtyard, and the natural flow would be to go from the courtyard to the street, then the bus stop, but the street is on the opposite side of the panel, away from the bus stop or the courtyard, which is just confusing for new folks, as it doesn't flow with the logic of the location, and seems like the buttons are all random, like the apartment. This doesn't help us make visual maps in our heads for remembering locations or button positions.