My (probably hazy) recollections are that the FCBA requirement looked at JSF-STOVL, JSF-CV, F/A18E and what was referred to as Navalised Eurofighter 2000 (NEF2000) as candidate aircraft. With STOVL, CTOL (in the carrier sense), STOBAR and Advanced STOBAR as operating modes.
The FJCA project was created by combining the RN FCBA and the RAF FOAS (Future Offensive Air System) requirements into a oner, as part of the ongoing Equipment Capability requirement rationalisations. FOAS was most definitely the GR4 replacement - sorry, future required capability(!).
The danger (IMO) of going down the mixed A & B route is that we will eventually end up with an orphan fleet, where - as has happened before with an aircraft that shall not be named - small fleets end up in the "savings measure" target sights.
Aside from the known divergence in commonality across the variants, I'd imagine the training requirements and syllabi would start to diverge as well, to the point where you'd end up with de facto three separate forces (Typhoon, F35A and F35B), with a concomitant reduction in commonality and an increase in DLOD costs.