1. There is a set precedent for how the Hunter's Exam is done, how Examinees are chosen. However, during canon time-lines there was an event (it was actually the very first event I name. With Killua) that sparked a drop in attendance. The show probably would have made it a 1-5 year drop, not a 20 year drop like I have. This drop is the major reason for the two options. Also, why would a "Magical Beast" want to become a Hunter? This allows players to create a Magical Beast character (nearly done with the CS now) which offers all kinds of room for characterization. No matter how intelligent, these are creatures called Beasts. There'd be discrimination within the current system that these characters could overcome or succumb to.
2. Yes and no. Certain circles yes, Most of the World, no.
3. Yes-ish. However, the Hunter's Exam is not fair. In the show there was 405 people in the 287th Session. Roughly 2/3's died prior to the third round started. There's also this to consider, again in the show in the 287th Session of the 7 (maybe 8) people who got licenses only two had Nen prior to finishing the test. Also, to be considered a full hunter there is a secret second exam/first real job "discover Nen and learn it." So all characters will have Nen by some point prior to the end of the RP, another point, if someone with Nen attacks someone without Nen and the one without survives...they'll have Nen. Now they could end up like seriously f***ed up, but they'd have Nen. (And again using Canon events for this part, the individuals who were the examples for this in some cases used this event to strengthen their Nen. They were just dumb. )
But realistically speaking, telling a group of people they can't attend the first part of the exam due to already having completed the second wouldn't work. Also, just having Nen doesn't mean certain rounds won't still potentially be difficult for them.
Also, there'd be a higher average of individuals with Nen compared to not. A) Normal applicants had dropped over a fairly long period of time. B) Several individuals were invited, so these are people chosen for their likelihood of passing the test. And C) The number of rounds where this advantage would matter, I'll be separating the normal individuals from the individuals with Nen. No confrontation no advantage.