I hadn't realised that they're using actual sloped grids of some sort but I reckon you could potentially achieve a slope with maybe a multi-story tilemap of sorts and then let the sorting order take care of the way the tiles display. This way you wouldn't have to come up with anything complicated for the navigation and collision.

I've just about got the hang of the maths around isometric tiles specifically in Godot and it's not obvious. Will probably do a write up when I'm happy with it all.