We need to investigate if we want this behavior or not, if we do not weld the base lod vertices, maybe we will have bad mesh behavior when not using the alternate skinning. The consequence of this need to be investigate to make sure we do not produce new bugs by doing this.
Import the sk from the attach Base.fbx file.
Add an Alternate profile from the attach file Base_Alt.fbx.
Some vertices that have different alternate skin weight are weld because the base model have the same weight for them.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-157658 in the post.