I think there are some major confusions about how the line and reservations are going to be handled.
1. mall lines and dedicated store lines will be handled differently. Depending on if the mall opens early enough or even lets people in at all at 7 or earlier. Flagship stores will have two lines.
2. I know this as a fact from an Apple Employee that "flagship" stores do get the most stock and will even leech stock from a nearby apple store just to maintain it's flagship appearance of having everything under control. It will most likely be able to fulfill all the reservations, they are also critiqued and held to higher and stricter standards than say, lower population mall sites. Mall sites/less busy stores tend to be more lax and will probably encounter some reservation/non reservation stock issues. But for the most part if you reserved at a flagship store (ie: like me, at one of the biggest stores in the US the Boylston St. location) you should be in good shape. Also, I know for a fact that people who reserve, at least in the case of the Boylston St. store, will be more likely taken cared of than those who didn't. It's harsh, but like I said, these flagship apple employees are held to a higher stricter code, and are more scrutinized to please the customers who reserved than to not. If you didn't reserve, and there's still a reserved line, you will be told to either wait, or come back at the end of the day or the next day.
3. However, although it says on your confirmation if you reserved that they will hold said product until closing time, that does not mean u should just waltz in all willy nilly at 10:45pm and expect after long and hard day to be handed a phone. Not saying you wont get it, but depending on how the day goes, it just might pay off to get it earlier than later.