IMO it all depends on whether the rest of the aircraft has "airframe scale" changes like YF-22->F-22 or X-35->F-35 or J-20 sn 200X -> sn 201X.
Because so far, outside of the intakes, MLG and exhausts, the rest of the aircraft's planform and geometry looks largely the same as the first airframe, which strikes me as more of a glorified difference between JF-17 PT3 and PT4, i.e.: implementing likely planned, "significant but localized" changes rather than a wholesale redesign of the aircraft.
I agree. The scope of characteristics encompassed in these changes, as far as we can say with the current collection of photos, are not as expansive as they might appear.
Caret to DSI shouldn’t affect overall flight characteristics, just the airstream conditions at the engine face in specific flight envelopes (and the engines themselves should have their own robustness tolerance margins for different airstream conditions).
Removal of nozzle flaps might be a decision to simplify. They’re also likely to have minimal impact in aerodynamic performance, and may even reduce some testing burdens if the flaps were removed specifically due to some adverse characteristics found during testing.
Landing gear also doesn’t affect flight performance and its critical parameters can probably be validated with full scale static models. I think if we had seen any significant changes to the planform or control surface schemes that would have indicated something more major.