With the simplest arrangement possible, Mordenkainen's Magnificent Mansion allows for 5000 sq ft. of space.
But suppose I was okay with slightly cramped quarters, would it be possible to arrange 25 cubes in a 5x5 rectangle, put another 25 cubes on top of those cubes, and then put walls at 6' 8'' (=20' / 3) in order to create 3 floors with 7500 sq ft of floor space?
The spell's description explicitly says:
You can create any floorplan you like, but the space can't exceed 50 cubes, each cube being 10 feet on each side."
That sentence unambiguously says that you're allowed to place internal walls and doors in the space wherever you want, provided the mansion's total volume fits within 50 cubes.
Furthermore, the spell's description also says:
The place is furnished and decorated as you choose.
So, even if your GM were to have a fit of madness and arbitrarily declare that the mansion can't have internal walls or that the internal walls have to run along the outsides of the cubes for some reason, you could simply declare that the mansion has an open plan, that its furnishings include a number of luxuriously-painted folding screens, and that your one hundred totally obedient copies of Viggo Mortensen servants can simply rearrange them to form new rooms on the fly.
Real talk time: The interior layout of the mansion is unlikely to be important in play. The mansion only lasts a day, and the number of creatures who can enter it is limited to the ones you designate when you cast the spell. This means that very few plot- or adventure-relevant encounters will occur within the mansion; it's mostly just a place for the party to take a load off and rest up in style - and in that case, the mansion's layout is purely a matter of flavour.
About the only time when a mansion's layout might be important to the game is if the caster deliberately use the spell to create an ideal ambush location or dungeon that they expect foes to enter - and if that happens, the ability to choose appropriate furnishings alone is already enough for them to make it a perfect ambush site or labyrinth for their needs, as heavy iron furniture already does all the things you'd want internal walls for anyway.
As such, there's really no reason for a GM to put more limitations on the layout of the mansion than are already on the spell.
You can both create a floorplan that is not based on overall square 10 x 10 x 10 cubes, and you can have interior walls.
In addition to the text only limiting you to the overall volume for your mansion to have to fit in 50 10-foot cubes, as proof, you can look at the map of the adventure The Joy of Extradimensional Spaces from Candlekeep Mysteries. This official module features a Magnificent Mansion that somehow has been made permanent.
Fistandia's mansion was created using a Mordenkainen's magnificent mansion spell and made permanent by Fistandia's own enchantments.
The map on p. 18 includes several areas that do not fit a 10-foot grid, like the entrance, which protrudes 5 feet, corridors that are 5 feet wide or the overall dimensions of the entire lower floor, which is 55 x 25 feet large. It even has outer areas with circular outlines.
If you follow the example from this module, then even the enveloping space in which you put your floor plan does not need to be in 10 x 10 x 10 foot cubes, because to encompass the dimensions of all three floors on 10 x 10 foot squares, you would need 83 such squares, and if the ceiling height on each level was 10 feet you would require 83 10-foot cubes, not 50. Even if you assumed there are only two layers of cubes, and each level is only 6 feet high to allow for some floors, you still would need more than 60 cubes. So the mansion would not fit the limits. The actual square footage of floors is is about 6,150 feet, not the 5,000 one would expect if all spaces were 10 feet high; at this square footage, you still could have floors that are about 8.1 foot high, comfortable enough for normal creatures, if all that mattered was the total cubic feet staying within 50,000.
Now, why even mention 10 x 10 x 10 foot cubes, if the only limitation was the total volume? I suspect that the adventure writers just did take some artisitic liberties, and did not in fact calculate total volumes. What would make sense to me is that the rooms must be of sizes that would fit into a structure build of 10 x 10 x 10 foot boxes. That way, you can have any shape you like for your balconies, but if they are not fitting into boring, superimposed 10 foot boxes, you are not using all the space you have.
In nearly all cases, if you use the mansion just to rest and eat, the actual detailed layout may not matter, because it is highly unlikely that you will experience tactical combat there, as you can control who may or may not enter. But there could be fringe situations where it comes to play, for example if you invite NPCs to stay, and some of them turn out to be traitors.
Rooms with windows to the outside are lit by the indigo miasma swirling outside the mansion, which colors everything in the room with its tint.
This is not mentioned anywhere in the spell description, so the adventure writers ad-libbed this. It furthermore is not even starting right at the boundary:
Outside, a swirling indigo miasma hovers 20 feet from the building on all sides. A creature that enters the miasma feels increasingly uneasy during the first minute of exposure. If it remains in the miasma, it gains 1 level of exhaustion for every minute it spends there.
None of this is in the spell description, so I think it is up to your DM if they want to adopt this idea.
I'm unsure how the above answer reached the conclusion "Yes" when it immediately quote the rule that says "No".
Each room must be at least 10 Ft wide. You simply cannot make one smaller, so 5 Ft is just not possible.
