One goal of BFR is Mars, from which you can only get back if you can produce fuel on the ground. Which kinda rules out RP-1 as propellant. Hence the need for a methane engine.

Unrelated to the number of engines here, obviously; just another point to consider. And if they end up designing a new engine they could just as well apply what they have learned in the meantime. Merlin is a very conservative design, favouring simplicity and cost over thrust. If you plan for re-using your rocket a thousand times, cost of an engine isn't that much of an issue anymore and you can prioritise other aspects.