Hi!
Indeed Game Master mode currently support levels with 1 region. If you developing a level in the editor i would suggest you to separate it in a few smaller levels - so all of them could be re-used with a different purposes. For your situation with second floor in building you probably would like to have it as separate level because in case you will need to make different states of that story - you could add them without dragging addition floor to it. That second floor with could also be used as "second floor" template for other situations you may need in GM campaign. Don't try to create all levels in the editor immediately suitable for your GM campaign. It much better to think of them as of generic level templates different GMs can re-use in their different adventures. Keeping levels small will allow you to reduce loading time and keep story modular together with having control of players party in a way of where they will go and when.
I absolutely understand the value of compartmentalizing GM maps into smaller modules, like having the inn separate from the town for example... but separating a second story of rooms from the main floor of the inn? That seems a bit excessive.
I do understand that, to some degree.... but there is a certain appeal having one single inn contained in the same level, without having to load in between. A single inn is small enough to not require multiple levels for "loading" reasons, or even managing player activity. It seem sort of silly to have to load in a second level just because the players want to see what's in the cellar, or to head up to their rooms.
I feel like giving the GM a full minimap is a relatively simple compromise that would really open up the possibility for GM control, even in small scale maps. It's possible it's more complicated than that... but having a "toggle" for a full map and a region map would go along way in my opinion.