The FC-31 v2 could very well be a "prototype" of the air force variant, albeit without much of the subsystems installed (but the J-20 2011 prototype didn't have electronics either).
The navy variant would have to be enlarged, and according to Internet chatter, the soon-upcoming v3 airframe would fulfill just that.
The FC-31 V2 could be a "prototype" of a hypothetical air force variant in the sense that the air force's requirements may be closely fulfilled by the airframe design, but as it is it would still lack the provisions for the likely subsystems that the air force would be interested in.
OTOH, for J-20, it had provisions for the 360 degree EO PDS installed beginning from the first prototype.
That said, I also disagree with Inst's assertion that lack of an EO PDS or whatever on the prototype stage means it would be difficult to install on the production aircraft, especially if the prototype is an early one -- i.e.: that a later prototype can feature the integration of an EO PDS or whatever other subsystem one is interested in.