This could be solved in part if we could have multiple instances of the Attendance module in a course. Then, in theory, you could restrict certain instances to a grouping.
What I do hope is that in addition to having more than one version in a course that parameters can be set on a group by group basis. We ran into this when teaching a course with 20 sections, and the Attendance was being taken by undergraduate interns; I think it took me a couple of days to figure out how to set that up, and it could have been so simple.
Attendance (plugin)
Groups/groupings and attendance
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