Multi-document transactions can be subject to Flow Control at prepare or commit time. However, by this point, the work and resources for the transaction have already been consumed, so further subjecting the transaction to Flow Control would prolong an already costly operation. The work for this ticket should be to investigate the appropriate means to avoid throttling prepare/commit/abort for transactions while still preventing new transactions from beginning when there is substantial replication lag.

prepare/commit/abort acquires this lock, so the fix for this might be a matter of excluding that opCtx at that particular point from Flow Control.