So, after a late night last night. And more digging, its becoming quite clear that multi-layer maps (not pbr texture slots) are not a trivial thing to get happening - mainly because there are many ways to end up with verts with multiple uv layers.
The result, is that exporting the uv layers while possible, is probably going to introduce a world of pain. The other potential downside, is that you will end up with more draw calls on an object with multiple uvlayers. I suspect it would be better to do things like decals, shadowmaps and so on, within defold itself, because each developer will likely ‘have their own method’.
Im adding a checkbox that enables embedding the extra data as a second channel only but this is likely to be inconsistent, due to the way people generate art in Blender - ie, one vert has multiple layers when mapping two sides of the vert to different textures.
Summary: Single texture/material for single mesh is going to be the norm - secondary textures can be added (check box), but wont be supported in the PBR and the data output may be inconsistent.