If I create a proposal and gain reputation from users joining my proposal, what happens to such reputation when the proposal is eventually closed, or when it progresses to a main site (after public beta)?
I am reasonably sure you do not retain the reputation when a proposal is deleted (all closed proposals are eventually deleted), but you do retain the reputation from a proposal while it is simply closed.
The code used to build Area 51 derived form our main Q&A, so we share of lot of the behaviors of a traditional Stack Exchange site. A proposal is roughly analogous to a 'question' on Stack Exchange, while the the proposal's "example questions" are roughly analogous to 'answers' on a Stack Exchange site. So when a question is closed (on SE), the reputation does not disappear, but once it is deleted, the reputation associated with it is also removed. Same goes for this site.
While I don't have access to the actual codebase to check, I'm reasonably certain this is how it works.