If an entity has more than 5 reportable transactions, not because they had any transactions over 10K... but because they were one of multiple entities where transactions were conducted by the same conductor that came in with a total cash amount of over 10k but not one entity transaction was over 10k. Could that entity be exempt from CTRs under Phase II even though they don't have any transactions to that specific entity that were over 10k?

No. To be exempted, the entity's own cash transactions need to meet the threshold.