Fwiw, I managed to write a plugin that calls an automation toolkit script and will merge texture sets at the click of a button. I can't share it cos I did it at work but it's not a particularly difficult thing to do so I imagine someone will release something similar at some point
You can open multiples images as layers in Photoshop. First export your textures from Substance Painter with transparency and a padding of 8, 16 pixels, etc depending on your texture's dimensions. Then using Bridge : Tools -> Photoshop -> Load Files into Photoshop Layers Or using Photoshop : File -> Scripts -> Load Files…