Is there a way to export layers into the same spritesheet on top of eachother?

It looks like you want to save each layer in a different file, you can use the CLI for that:

aseprite -b map.ase --save-as map-{layer}.png

This works since v1.2-beta1. More details in the docs and –save-as. (Or en v1.1.13 you can use –split-layers.)