Good to see people being warm to the idea.
1) My view on this would be, every time you make a change you get a new serial, this is kind of a hard fact of the solution. This IMO is the only 100% reliable and fool proof way of ensuring people have the right stuff, with the minimum of confusion. It will be up to the author to decide whether or not the addon is backwards compatible, and to flag the old serial as depricated. The old entry in the central DB will have a pointer to the new serial, and it will be a linked list in that way. The thing to keep in mind is that the process will be painless and a serial is just a number, we would probably have an enormous capacity in terms of serials, like several billion numbers in 10 base.
2) Certainly I see your point, however as it looks right now, it will be up to the addon makers to decide if they wish to break up their addons into several standalone PBO's and to request serials for each. That's the problem of allowing a breakdown of an addon/mod, you often need to grow each individual piece, and need a lot more testing to ensure each eas truly capable of running without the other. Having said that, it is theoretically in BIS's capability to write an addon/mod interpreter which automatically has a capability of breaking down an addon into standalone pieces. (scripts being the only immensly unpredictable factor, especially if an addon maker does not consider that the pathscould change) Theoretically. I am certain BIS doesn't have the time to do this, but I hope they implement a centralized serialization and distribution/acquisition of addons!