Goal:
Assess how we can improve/ clarify the layering between OpQueueBatcher and OplogApplier. Furthermore, investigate and address the remaining TODO's that reference this ticket in the codebase.

Background:
There are several places in the code with TODO's that should be addressed for this ticket.
`git grep -ni "SERVER-43001"`
With the changes outlined in SERVER-44303, the remaining TODO's can be investigated and addressed in effort to improve and clarify layering.