Substances don’t quite work in beta 11 with the Standard Shader, right? They seem to confuse the Dynamic GI, which doesn’t seem to recalc properly when the scene changes, especially with reflection and the new cube maps.
Has anyone else experienced this?
I think I’ve read fom someone from Unity that so far in the Beta you will still have to render your substances and merge the Specular Greyscale and color map in Photoshop. Also you need to tewak your values a little as the two shaders right now don’t sync up perfectly.
shouldn’t have to merge anything in photoshop, in substance designer you can RGB-A merge the specular color and the gloss into an output.
you are correct the spec/gloss shaders in SD and unity are slightly different but from my experience its pretty close.
if you are working with metal/rough workflow in SD, and using the Metal/rough to spec/gloss conversion node, then you need to make adjustments to your specular color (from real world values) and level out the gloss a little bit. That conversion node is not a direct conversion, it just swaps the metalic specular color from the base color map over to specular color map. It outputs a default specularity color that isn’t always correct.
anyways, I don’t think this has anything to do with what the OP was talking about though. Sorry 
I have noticed a lot of issues with substances in the unity 5 beta… currently am baking them out because it’s really buggy.
I’m using the Lux4SD shaders in substance designer which seem to be pretty close, and use the same map setup as the unity shader.