Update: the bug will be fixed in XenForo 2.1.0 Beta 6. Based on their instructions, I have made the necessary changes to the option XML to workaround the issue and support the XF2 fix when it is published. Not sure why they labelled it Not a Bug.
The updated XML will appear in build 003. After applying build 003, using XF2's add-on Rebuild should resolve the issue.