We've encountered exactly the same issue here.
Our hope was that the issue of being able to import group data to WebPA would be solved in Moodle 3.0 (based on the description and some of the comments associated with MDL-41725). However, since it looks like use of the LTI memberships service requires the LTI client to offer up some sort of Registration URL - which, to the best of my knowledge, WebPA doesn't do - we're still completely stuck. What's even more frustrating is that apparently BlackBoard can import group data without issue.
If anyone has any insight I'd really be grateful if it could be shared.