The likelihood of this happening is extremely remote. It happened in Boston only because the weather was comically bad, and most of the pros dropped out or had hypothermia. In any event, if we're positing a non-elite finishing in the money, it's clearly a better situation for the non-elite to have started with the pros and simply not had his own bottles, vs. starting with the masses and having a faster chip time, like what happened with Wesley Korir at Chicago in 2008. And starting position is a non-issue. In New York, if you're sub-2:35, you can start with your toe literally on the starting line if you want to.
I'm not sure what you mean by this. There are no rules requiring that all athletes have the same on-course services. In fact, USATF in 2007 announced that only A-standard athletes would get private bottles for the Trials. There was outcry over that, and the decision was reversed, but mostly it was because the decision was made unilaterally by USATF. The local organizing committee, which wasn't consulted about the decision, had been totaly prepared to provide private bottle service for all runners, and they said it was no problem. So it was apparent that USATF had made the decision simply because it wanted to send the message that B-standard runners were less deserving or something, and not because of any practical difficulties with managing private bottles. Notably, though, nobody was arguing that it was illegal to have bottles for only some athletes or that it would be illegitimate to make such a distinction if there were legitimate logistical concerns.
This has never been an issue. The pros get to put their toes on the line, and when the gun goes off, they're running 5-minute pace. They are always clear within seconds. It doesn't matter how many people are behind you; what matters is how many people are starting at the same speed as you. The dangerous starts are the ones with really deep pro fields, like Valencia or the Half Marathon Champs in Cardiff where Kamworor fell in 2016.