make_duplis_group is using lay bits to check whether an object is visible. We need a design that integrates this with collections.
A few options:
- Allow users to instance entire collections instead of groups. This would literally make groups obsolete.
- Improve the 'only render' visibility filter per collection, and have users relying on this alone.
(2) will happen eventually, so if this is an acceptable solution, it's easy to move forward.