Bigotry is not tolerating different opinions.
Bigotry is a lot of things, small and large, and it includes prejudging others based on your
opinions, not on the actual facts.
I do not see that in a system that judges others on their own behavior.
Nor do I. And we have a system that does that, in principle, with varying degrees of success. It is called the Criminal Justice System. But that's not directly what we are talking about here.
I understand you make a distinction between the right to keep, and the right to bear arms. So do some states, which is wrong (but that's another argument, something for a different thread, I think) which is the reasoning behind the existence of permits.
Now we come to what is, and is not justification for the individual to be granted a permit. This is stated in law. Also in law are the specific disqualifiers. Behavior(s) that do not meet those disqualifiers
should not be used to disqualify an applicant.
However, what those disqualifiers are can vary widely, all depending on the applicable laws. This is where the writing of essays, character references etc., comes in. The governing laws say things like "demonstrated responsibility" or "good character" or other language with the same general intent.
Now take Mr Doe you have created. He's borderline fail in several areas of his life. But not to the point where he has been convicted of anything, or judged incompetent through due process. Although he isn't a prohibited person, he doesn't seem like a good risk. Right?
And he probably isn't a good risk, going by "the numbers". However, he might be the kind of guy who is poor or borderline fail at some things and competent, or even hyper-capable at something else. Perhaps safe and sane gun handling is one thing he is actually very, very good at. You simply don't know.
How do you find out? There seem to be two schools of thought. On is that you create a set of standards, some kind of test, which must be passed before approval is granted. Lets call this "may issue".
The other is that absent the legally stated disqualifiers, LIFE is the test. You accept the risk as part of the price of freedom. Call this "shall issue".
With John Doe, by looking at things that aren't legal disqualifiers I feel you are judging a book by its cover, or not heeding that little warning in all the ads that want you to buy stock "past behavior is no guarantee of future performance,..."
This is the essence of "may issue"
I also think it is a mistake to look at insurance companies and their rate practices and apply it to anything else. For one thing, they are in business to make a profit! I spent more than a little bit of my life working in the industrial safety field (mostly the "field" part), and I think I have a basically sound understanding of risk assessment and the graded approach, among other things.
Insurance companies have their own approach, and I assure you it is not 100% about safety, it's about calculated risk, both individual and in general terms for their company. Clearly this works well enough for them to not only stay in business, and profit enormously, but I don't think it is the way we should look at fundamental human rights.