I think the dowel idea would work, never thought of doing it that way.
In the past (and typically) we score the lower layer with the outline of the next layer on top. So if you have a mountain and the top is 253 then the layer 252 will have 253 scored into it. We also label it so 252 says its topo 252 and that the scored next layer is 253 and then layer 253 is to 253. Then just glue it up! if you have multiple 253’s then we just label them with decimals or letters.
In this case for the $500 model it was aligned to the uphill corner because everything slopes down. so basically all the layers will the same corner and it is easy to line things up. I didn’t work on this one personally but my colleagues did and I will try and get more pictures (with details!)