Yes, cutting some parts with different thickness to layer on or slot in is what is lacking from most kits to get away from the 3D nature.
My personal interest would be to get them as a base to build on, as for some reason I really suck at building a solid basic box structure (really!) or cutting straight windows/doors, sides,... But as Thunderchicken said, they are a bit too expensive for that.
Still, I might get one of these to experiment with and see if it's worth the trouble required to make it more 3D. And Jimbibbly's are definitely on the to buy list. I also got the Griffin house from Fenris Games, which looks terrific, though the number of components in the kit is very intimidating.