Prior context (for anyone stumbling across this thread) is this workflow:
- Create a complex vertex animation in Blender.
- Export to MDD.
- Import the MDD back into Blender as shape keys (morph targets).
- Export to glTF.
This bakes out the MDD file into keyframed morph targets, which as the OP writes would increase its size. I don’t think Draco will help in this particular case. You can compress this glTF file with gltfpack, that would be my suggestion.