I don't know if this is the real historical reason, but if you're doing something 2.5D, isometric, at with 2D graphics, at anything other than a 45 degree angle, then anything larger than one square creates clipping problems because part of it should either be behind another sprite on a square whose closest vertex is closer to the camera than the furthest vertex of the forward element. Z-ordering things on the ground between those elements gets even trickier. Making each building (or part of a building) stay within one square is by far the easiest way out of that predicament.

It's not aperiodic, but I remember a roguelike game on a hyperbolic surface, resulting in more than six neighboring cells in some dungeons.

Check out Townscaper.

https://andersource.dev/2020/11/06/organic-grid.html