Ok, I tried adding the alpha into the base color texture itself, and it works fine as a transparency in GLTF. Here, all body parts have OPAQUE alphaMode, as we will apply alpha mapping to each body part anyway.
But my worst fear is true: the render order is out of whack.
Hi, is there a programmatical way of fixing this issue. I am also facing the same issue. In three js, i have created a object with the alpha map. When exported in to GLTF Format and imported the same in the blender, the alpha map is missing. How one should fix this issue.