Custom PBR Metallic/Roughness Shader with Premultiplied Alpha
Have you tried texturing glass in Substance Painter?
By default Substance Painter there has only one semitransparent shader - Alpha Blending. With this shader, with increasing transparency, reflections and speculars also become transparent.
To solve this I suggest using a custom shader with support Premultiplied Alpha. The videos show how to install and use it.
