Hello there,
I've been trying to create a one-material set-up for my game involving an atlas texture. For my modeling I use Blender and export everything using gltf/glb-files; for my textures I use Krita and pngs. There are two problems I keep running into:
Whenever I try to make the material transparent in Godot, it keeps reverting to non-transparent at frequent intervals, even though it hasn't been overwritten in Blender. That's a bit annoying but not detrimental.
Upon changing it to transparent, even sub-textures that are fully non-transparent become transparent in-game and in the editor. What's curious is that they don't turn transparent altogether, but only in weird locations. For example, I am then able to see into my rooms from the outside but not always able to view the outside from inside, despite the fact that all faces are mapped to the same part of the texture.
I could, of course, create a second material that includes only transparent textures which would presumably circumvent the latter issue, but my concern is mostly with understanding why this happens.
Here is a visual example of what I mean. All objects visible in the Godot scene below are mapped to a non-transparent texture, but are nonetheless partly see-through.
With material transparent:

With material non-transparent:
Atlas texture:

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