Let me add that this issue is occurring because in the packs there exists PBR textures that don't fully match the resolution of the base texture.
As a result for some reason the texture atlas stitcher expects the UV size of the PBR texture to match the base texture and causes this weird problem where a texture can be eclipsed by a different texture, no matter which texture type it is (Diffuse, Specular/MER, or Normals/Bump)
Still occurring in 18w47b...
Pasting my thoughts expressed to the poster, from Twitter
I doubt strictly embedding it all would be the ideal solution. The ideal solution would to have an internal database storing those references. This is a win-win situation because mods starting in 1.16 (ideally) also add dimensions through datapack means.
This way, everything still in storage and anything that's a reference still remains a reference. If the dimension itself is fine but one of the references errors, it simply has a backup for that reference, instead of defaulting entire dimension to the backup.