My initial motivation was to make cyberdiscs hitbox in form of actually a floating disc, that is much harder to hit with horizontal fire line, than, let's say, a Reaper hitbox. But if you will hit it from above or below - it's an easy target as well. Considering it's a flying unit - it makes a lot of tactical gameplay meaning.
Also, if we take iconic example with sectoid hitbox, on fixing like @Reaver is proposing, we will get its hitbox not that different from muton's. But they are very different in sizes, judging ufopadia and battlescape images… Making muton is a target, that is much easier to hit, compared to smaller enemies, would make interesting balance options, considering its high armor value.
I can go on with more examples like that.
Sectoids already use a smaller column (2) while snakemen use a larger column (4) and the rest (floater, muton, ethereal) use a "medium" column (3). My hitbox mod fixes this by boosting them all to 3 for sectoids, 5 for snakemen, and 4 for the rest.
You can already make the cyberdisc hitbox match its model simply by making it shorter, but it causes a bug in which if it is standing on elevated ground, melee attacks can't hit it. The hitbox height it has is the bare minimum to avoid the bug; shrinking it by even one voxel will make it commonly unhittable in melee. But soldiers have no significant difficulty in hitting the smaller hitbox with ranged weapons, so aside from the melee bug it works great.
I think we'd have no major issues with hitboxes if the hitbox bugs were fixed:
1.) Small units have their weapon height based on hitbox height, and it is correct only for soldiers, and wrong for ALL other alien races.
2.) Large units must have a minimum hitbox height in order for melee weapons to function correctly (unless they never stand on inclined terrain).
3.) Shot angle has a very high odds of hitting almost exactly dead center where the soldier is aiming, roughly equal to their list chance to hit in most cases. Then if it doesn't go dead center, it goes straight to stormtrooper accuracy more or less regardless of the shot's list accuracy (and this can still happen at 110%+). This means their odds of hitting a bee off your nose at 100 tiles is not significantly different than their odds of hitting a snakeman at 5 tiles, and no that is not an exaggeration.
4.) This might be the most difficult one to fix, or maybe it isn't: sometimes a soldier simply aims along a trajectory which does not intersect with the target's hitbox. This is most common with: diagonal shots esp. with elevation differences (which can be mitigated by making perfectly orthogonal shots); strange target hitboxes esp. against terrain or if target hitbox is very small/off center; having tile hitboxes in between the shooter and the target (occurs differently but not necessarily less commonly with OXCE's off-center shooting, can be mitigated by using OXCE's alt-fire). I don't know much about how this stuff works but I think it was either SupSuper or Warboy who showed me the function in the base code. There was a list of tile positions it seeks to find an eligible trajectory, and perhaps fixing it is as simple as expanding the list.
If a soldier aims along a missing trajectory, the most noticeable thing is that the shot will ALWAYS miss UNLESS it is a stormtrooper accuracy shot which gets lucky. All bee-off-the-nose shots will take nearly the exact same path and miss their target. This means that the higher a soldier's accuracy is, the lower their odds of hitting the target. The only way to fix it is to move either the shooter or the target to a different position.