You were actually quite clear already in your previous description. The suggested formula can be easily extended by defining more grading schemes and adding corresponding flags. It seems though that you only need one more flag in the course level, for the final, and so the formula in the course total may be just a little bit more complex. The homework assignments may be handled in a similar way but separately in the Homework category.
Indeed older versions have this "exclude" feature. I never used it myself. I wonder how this feature knows in what relative fashion it should redistribute the slack. If it's a fixed way then the feature may not be very useful to anyone who doesn't follow this predetermined scheme. It wouldn't be surprising if this feature was intentionally omitted from later versions precisely for this reason.
Isn't this how most teachers handle excused absences?
Perhaps, but since now we are Moodling we may as well reconsider what most teachers do. Personally I don't see much point in mid-terms, all the more so if they give rise to many exclusions. If the Final Exam is necessary for a final grade there should be no exclusions there. The Homework component can have a built-in make-up element (e.g. 10 best of 11); in addition, each homework assignment can be available online for a whole week (this way it won't be enough to be sick for a couple of hours to get an exclusion; one will have to be very sick the whole week(!) and still the first such week will already be covered by the make-up assignment). This should cover all standard exclusion cases including required accommodations for special needs. If there are outstanding issues at all they are very few and at any rate they already deserve manual handling by virtue of being outstanding.
So perhaps the exclusion problem may be effectively resolved by restructuring the assessment scheme. Just a thought. 