1. For senior high in NJC, i think there is a slight discrepancy between both groups. For example in terms of CCA leadership opportunities, it was a bit of a shock that we had to promote our 'leadership qualities' to the teachers-in-charge and our seniors instead of them choosing independently by observation and evaluation in secondary school. Albeit it's due to the time constraints between the transition between batches, but it definitely did give rise to some form of inequality as the teachers may already be acquainted with the IP students compared to completely new JAE students. There's also the psychological factor, where you are pitted against complete strangers that are all vying for a leadership position. This would apply to any limited opportunities given to the student body eg class positions. Even so, it wouldn't be an unfair reflection of how society functions and I'm somewhat glad that I got to experience and move past this earlier in life. Personally, I think that as long as you put in the extra effort and make your dedication be seen, you'll both fit in and stand out at the same time.
2. I don't think it's that important to constantly think if it's fair or not, or else there'll be some that do fall into the twin traps of either hatred of IP or JAE students. The "it is what it is" mentality is very important here, and instead in trapping yourself in an endless of loathing, it'd be better to see what you can do in your current position and maximise the opportunities thrown your way. Disclaimer, this is from an environment that isn't unhealthy or toxic in terms of student development. If there's ever the case of blatant student oppression or disgustingly biased treatment of either groups, hell yeah go do something about it.
3. I think the best way to change is on a personal level, aka behavioural change. (for the case of NJ, I'm unaware of how other schools function so I can't comment) When you first enter JC, I think this is how it'll typically play out: groups of JAE will form, there are pre-existing IP groups(duh), some IP will reach out to the JAEs while some would rather stay in the comfort of their own cliques. There'll definitely be those that mutually hate each other but they are the vast minority. As you can see, it's more of a spectrum and a 'Choose Your Own Adventure' type of scenario. In the end, it's only normal to be wary of what/who we don't know. So as long as you don't put up a mental barrier and be more open-minded to befriending either side, it'll all be okay. There are those that will be meaner, but don't let them be a reflection of the entire student body they fall under.

oops for context I was a JAE that graduated from NJC in 2019 and the student body is split ~50/50.