You say "reservations", but I take that to be tickets. If that is the case, you are not connecting at JFK, but rather simply transferring between tickets. MCT is simply a carrier's willingness to accept the risk of a misconnect. It has no applicability if you are on two tickets.

1. B6 is unlikely to check your bag onto CX. Thus, you will need to retrieve it at JFK and check in with CX.

2. If you no show for your CX flight, you have no protection. Your ticket will be cancelled. Depending on the ticket's fare rules and the charity of the CX agent, you may have to purchase a new ticket.

My general rule of thumb is to allow 2-3x the MCT when you are on separate tickets. That is certainly not met here.

All disturbing stuff about your travel consultant. If the TA doesn't know this basic stuff, ditch him.