Many teachers have expressed this concern, which is merited to some degree. You should grade on the regular curriculum which has been compacted. In our opinion, grades should reflect mastery of content and not time spent in a subject area.
When you do substitute independent study, it should not be graded. Some qualitative, holistic evaluation of the work done would be preferred.
Note: If you find that students are not using their time for alternative study wisely, you should talk over the problem with them. You might reiterate the concept of compacting, and explain what the next step would be if behavior doesn’t change (such as a parent meeting). Compacting represents a radical educational departure for most students, and it takes time for them to adjust.