There will be mess with byes again just like in NAC...First of all: 112 or 128 participants, 7 rounds over 7 weeks... Yes, there WILL be players dropping out. This doesn't have to be due to bad manners. There are a lot of things that can come up over that timeframe.
Second of all: It simply doesn't matter at all. I don't know yet how Swiss System at that scale will work out for AoE2 - it has certain advantages and disadvantages. But one advantage certainly is that it is very flexible with regard to number of players. Average points per player does not have any impact. If there are 60 people with 1 point and 60 people with 0 points or 50 with 1 and 70 with 0 - it's all fine.
Unfortunately, no system exists that can "ensure that the top 16 is the corect strongest 16 players". The most popular one (I assume) - single elimination - is probably the worst at it.