I'm relatively new to using Toolbag 4 and I can't seem to find any resources that handle transparency masks for objects that aren't purely made out transparent materials. I decided to test the transparency exports from Substance Painter by setting up an old scene on Marmoset, and unfortunately I can't get the transparency export to work at all. What I get is usually either a completely transparent glass pane, or a completely opaque one. Many older guides for Toolbag 3 refer back to Additive transparency, but all that's left in 4 is either Cutout or Dither, and the only way I've gotten my mask to work is to use Cutout in combination with a refractive transmission map.
Here you can see how the dirt and minor reflections in Substance Painter seem to be completely gone in Toolbag 4, despite all texture maps being unchanged from the SP2 export. Keep in mind this is with raytracing enabled and 8 transmission passes.
The transmission and transparency setups are what you see here. I greatly appreciate any feedback that can lead to a better import to MT4. Absolutely adore this program so far, but setting this up has been a bit more difficult than I could've anticipated.