I did a little more investigation and I think I found what might be causing the issue. I investigated a random file of yours called Tree09.glb.
The baseColor_2.png of that file texture actually does contain transparency (about 76% of its pixels are transparent), so the alpha information seems to be present in the PNG.
However, in the GLTF material that uses baseColor_2.png, I can see that the material has doubleSided: true and the baseColorTexture, but there doesn't seem to be an alphaMode such as MASK or BLEND (or an alphaCutoff).
So it looks like the texture contains the correct alpha information, but the GLTF material may not be telling the renderer to actually use that alpha for transparency. This could be why the transparent parts are showing as black/opaque in Blender, Godot, GDevelop, etc.
I could be misunderstanding something, but I hope this could help identifying the issue.