We currently do not copy over the Config folder when we are packaging a plugin for inclusion with a packaged game. This is likely because we haven't supported plugin config files in the past, but they now work properly as of 4.16 (see [Link Removed]). We should update the packaging code to include these plugin config files. Current workaround is to manually copy them after packaging.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-52655 in the post.