Plugin mount point registration doesn't mount paths relative to both root and engine, only relative to root while most other Engine directory mount point registrations include both ../../Content/... and ../../../Engine/Content/...
The DefaultConvertToRelativePath has a path in the while loop where it will try to resolve against the binaries directory which results in plugin assets in the Engine directory to resolve to ../../Plugins/... instead of ../../../Engine/Plugins/...
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-40317 in the post.