That's true. Yet, there are still odd situations in the game. For example, when you encounter evil Maxim and he transforms into that shadow monster. Afterwards, the only way to progress the game is to go back to the same exact room where you fought Shadow, except in castle A. Then you'll find Maxim there, crouching like he's wounded. But there's no reason why Maxim would show up in that room if you go with the "two castle existing simultaneously" interpretation. However, the developers seemed to think this was logical somehow because absolutely no clue is provided that the player should go back there. Whichever interpretation you go with, things don't add up. It's really bizarre.
Actually I don't think it's that difficult to understand, I think the technicalities are being overly thought out. Characters move in between the 2 castles, they can't be in two places at once, but Maxim can "jump" between the 2. The way this would work is in the example of the Maxim fight you've referenced; The "evil" side (B) takes over during the fight, when it gets overridden by the "good" side (A), he's back in the first Castle (A).
However, by the end of the game, the 2 castles (layers A & B) are overlapping, hence Maxim is in both and essentially the same event is happening except that in B, you fight the evil Maxim. Which is why the good ending happens in Castle B.
However, by that token it's a game and certain events will only prompt when you reach a specific screen. This is not so disimilar to SOTN, while playing as Alucard, Maria waits for Alucard in multiple locations at one instant. Classic example being the spike room and ending room, or the Holy Goggles room/ ending room/ spike room. In reality she could only be at one of those locations, but different in game events occur in order to prompt different events to occur.