I'm also not sure if the inverted rooms are centered the same way on screen. By that, I mean that some pixel rows visible in the normal castle might not be in the inverted one, forcing at least a bit of mapping for every room in the inverted castle, not to mention all the areas with different color palettes.
As for the grid, I wouldn't say it doesn't fit it; rather, I think it's caused more by the way that rooms are shown in-game. By that, I mean that a room might appear to be quite irregularily-shaped on the minimap, but when you're actually inside, the game seems to adjust the actual boundaries of said room (the point at which it stops scrolling) at least at the farthest limits in every direction, essentially becoming the smallest rectangle inside which the room can fit. That's why I *think* there seems to be more room beyond a wall or roof even though the minimap says it shouldn't be.
Personally, for Harmony Of Dissonance I just extended the borders by an integer number of screens to make them look good. For example, the Chapel Of Dissonance shows a lot of open sky with moving clouds outside its walls, but if I followed the grid of the minimap to the letter, then the room borders would stop right next to the walls and roofs of the Chapel and the sky is mostly left "off-screen".
And again, amazing work! Sorry I haven't had any time to spend on this; I hope you're not feeling too let down since the project has lost the steam it had when it was first started.
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"With the first link, the chain is forged. The first speech censored, the first thought forbidden, the first freedom denied, chains us all irrevocably." [...] The first time any man's freedom is trodden on, we're all damaged. - Captain Jean-Luc Picard
B*tch, meet reality. Reality, meet b*tch. - Me