Are you talking about isometric art? In this case I'd imagine it's just a bit of dev trickery, it depends on how the tilemaps and navmesh on either Godot and Unity are rendering but you could conceivable just put in a plane or something and connect it up to the navmesh so it all bakes correctly and do it that way.

It's all about poking the engines and learning how their insides work. Once you have a detailed knowledge of that it's easy to even create work arounds for problems you're facing unless there's a heavy amount of maths involved.