It is frequently stated that the side-by-side cockpit and crew-escape capsule were Navy requirements. I do not believe either to be correct. It is true that 1) the F3D and F6D had side-by-side cockpits and 2) achieving minimum length (a Navy requirement) favors them (but was not required on the F-14). However, there were TFX proposals with tandem cockpits prior to the down-select to Boeing and General Dynamics, Republic's for one. A picture of a Boeing display of TFX mockups and models includes a tandem cockpit mockup next to the side-by-side one. That strongly suggests that side-by-side seating was not a explicit requirement. Note also that while the F6D had a four-foot diameter antenna, meaning frontal area was primarily dictated by it and not the seating arrangement, the F-111B's was limited to three feet (I'm pretty sure that the F-111A's terrain-following radar antenna was wider).
With respect to the crew-escape capsule, while Douglas and Vought had at least suggested them to BuAer, the Navy doesn't appear to have had any interest, certainly not compared to the Air Force's, which was arguably more concerned with survivable supersonic ejections than the Navy. The B-58 and B-70 crew sat in individual capsules and the B-1 prototypes flew with one that housed all four of the crew. My guess is that the Air Force was also concerned with survivability in the icy waters of the North Atlantic in the event that a crew had to jettison an F-111 during a ferry flight to Europe. The Navy was far more likely to have a rescue ship or helicopter responding quickly in that situation.
Finally, McNamara's direction that settled the requirement deadlock on 1 September 1961 was that "Changes to the Air Force tactical version of the basic aircraft to achieve the Navy mission shall be held to a minimum". My guess is that one or more of the subsequent proposals included the side-by-side escape capsule as an unrequested feature that the Air Force decided was an excellent idea.
Does anyone have a TFX requirements and/or proposal document that proves otherwise?