I am having this same issue. It worked yesterday. What I did was bring in my mesh with PBR - metalic roughness. Baked the mesh maps. I then in shader settings, changed to pbr-metal-rough-with-alpha-blending, then added an opacity channel. On the material layer, I added a material, added a fill layer above it, set the opacity to 0. Added a black mask then used a brush to make holes in the mesh. When I went to export textures, under texture sets, the material had the opacity channel map added as a texture to export.
I did the same thing today and now it will not create a opacity texture. The only difference was that yesterday, the pbr-metal-rough-with-alpha-blending had behind it (outdated version). Unfortunately when I went back today to do it again, it no longer states that it is outdated and I am wondering if that is the problem.