It's easy to check it yourself. The room counter is displayed in the pause menu.
In fact I did just that shortly after posting and felt like a dummy for not doing it before posting, but thank you for your prompt attention to the matter.
Yes, they count... So where am I missing rooms? ? ?
I hate this mechanic lol
Edit: So, there are not, an equal, number of rooms, in the regular castle, as in, the upside down one.
I cannot believe I have been playing this game since it came out and have not realized this.
There are 6 more rooms in the upside down castle.
Regular Castle, 942+3 = 945
Upside Down Castle, 948+3 = 951.
Welp, now I know as they say