The MCT represents BA & DL's willingness to accept the risk of a misconnect. Nothing more. If you are willing to accept a greater risk than the two involved carriers, you may do so by booking separate tickets.

Carriers tend to establish the shortest time period which they can reasonably meet. Hence, unless you know better, going under the MCT by booking separately is asking for trouble (which will leave you completely on your own to get to your destination). No duty of care and possibly not even rebooking.