As far as I know, one object need to use one texture, you can not export an object with multiple texture files...Just to clarify : an object (.gltf) is composed with several mesh (wall, door, roof, windows...) and material (opaque and blend)
Same object (.gltf) with multiple material (one for glass and the other for wall).
Off course, you can seperate windows mesh from wall mesh and assign a glass material. These surfaces will be no longer assign to texture (wall material).