Could you expand on this? I'm struggling to imagine a realistic scenario where visual confirmation of a target would be a requirement. I also don't see why an F-35 is at a major disadvantage inside visual range of a target. (FYI Visual range is farther than short range air to air missiles and much farther than gun range.)
The AIM-54 Phoenix was used 2 times with exactly zero kills, because of ID concerns[1]. You don't just go around firing missiles to radar tracks you can't identify.
[1] by the US, Iran has used it more with more success.
The article you linked makes it sound like sensor and rocketry failures on some platforms that were retired 15 years ago, nothing to do with a general fear of BVR missile use. Also I believe the willingness to engage unidentified radar tracks has more to do with the nature of the conflict. I doubt the same restraint would be shown in a war against a near peer foe.
Roughly, because the stealthier an aircraft is the less maneuverable it an be. Also, you need ammunition for a dog fight, which is mostly carried on the wings negating any stealth characteristics. And large internal bays make an aircraft less maneuverable.
There was not a lot of air-to-air combat between near-peer air forces going on in the last decades, was there? What little air combat we had was between top notch fighters and crew, supported by AWACS and all the fancy stuff that comes with it, against badly trained and coordinated almost obsolete fighters. Anti-air systems were the main concern.