Hi Wes,
I don't think that works well at all for architectural workflows, but then again, the explanation is so confusing and technical that I'm not sure that it really implies.
Architects will come in with a merged mesh that contains multiple textures. We want oreplace these textures with better substance textures and then export a single mesh and a single map of all these textures together. IT seems to me that your solution will be totally useless for this worklfow? Please correct me if I'm wrong.
Obviously, architect will use Susbtance is a totally different way than game designers and modellers. But please, I highly suggest you look at the workflow of an architect that wants to bring his Revit model to Unity and bake through Substance in 3ds Max. We are trying to parse through all your complex documentation to do something somewhat simple and it's a huge pain. And then things like this happen that make the product almost too much trouble for it's worth. I don't want to spend 3 hours merging 150 textures in Photoshop.
Anyhow, I hope that whatever solution you guys implement will work for everyone and that I can start using Substance again. Until this merging problem is resolved, I'm going to stick to my old ugly textures.