That does become a bit of a problem, although it's one that's relevant for multi-cell creatures of any height past the first. But of course those then become the exception rather than the rule. Still, something that has to be dealt with eventually.
How important is that to your goal with the game eventually?
Obviously, given the source material, most of the enemies are going to be humans or at least roughly human. Are Dragons, Giants, and Mammoths going to be in? Are they important to have in a useful way?
Now's the time to change rederers if you're going to do that, but it's also a giant pain to change renderers completely. So I understand if you don't want to do that.
Dragons, giants, and mammoths are the reason I wanted multi-cell entities to begin with. Also ships and huge wagons worthy of queens.
I was thinking of having entity 'parts' where each part is cell-sized and is linked to the other parts, which would allow for 'deformability' since you could literally break a vehicle or tear a creature apart into pieces. I've seen it done in an artificial life simulation (Evolve4) and I think I can figure out a good approach to apply it to 3D voxels.
Or I could use DF's quantum tile concept and avoid multi-cell entities altogether.
Maybe we should just assume one cell is 1*1*2? Or do it the DF way and not think too much about this?
It's tempting, I know why Toady chose that approach now.
Maybe a combination of increasing the cell size to accommodate humanoids and linked entity parts for larger creatures?