Here's a workflow for taking a model that was created and UV unwrapped in Blender into Substance Painter to add textures (in particular, opacity or glass) and then exporting the textures from Substance Painter and using them in Blender.
In Substance Painter:
1. Choosing pbr-metal-roughness-with-alpha-blending for the glass shader
2. Adding an opacity channel for the glass
3. Export settings to export the opacity map (starts around 8:00)
In Blender:
1. Node set-up for the opacity map
2. Changes to the glass material (ie. alpha blend, screen space reflections)
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