You are assuming that the aircraft we are seeing right now (FC-31 v2) is in any way meant to be reflective of what the air force or navy's requirement may actually be.
We call the FC-31 as a prototype, but I think that term might not even be accurate. Instead, I think it is better to view the FC-31 v2 as a flying demonstrator without any intended subsystems as part of the aircraft, but rather offering the airframe as the basis for whatever subsystems and modifications that the air force or navy may want to put in.
So in reflection, I think I see the FC-31 v2 as not even a prototype, and is in some ways even less developed for air force or navy's requirements than the original J-20 s/n 2001 was for the air force, as the original J-20 prototype was at least developed with provisions for the air force's own requirements to guide them whereas FC-31 v1 and v2 were both done on SAC's own dime, without any meaningful input from the air force or navy.
OTOH, now that the navy has supposedly chosen the FC-31 or a variant of it for its naval fighter, if that is in fact the case then we should be seeing an actual programme standard prototype for FC-31 (or J-31 or J-35 or whatever it's called) emerge some time in the foreseeable future which should be equipped with the provisions for the subsystems that the Navy may be interested in.