This may be a bad idea for a number of reasons: it might be a bit too game-y for an ARG, it might undercut the sense of actions having consequences, and it might encourage more grinding/scumming than you want. And I suppose that, once it gets out of Alpha, I could register a second account and explore the other story branches that way. So, if any of those factors make it impractical, that's fine, I'm just putting it out there.
You've got everything pretty much correct! Your choices and actions are permanent for a given account. This is partly to give weight to the decisions you make, and partly because the systems will end up pretty interrelated and it'll be hard to figure out what resetting your progress means.
Once registrations are open, you're welcome to make a second account as you say. Eventually we'll have stuff for sale; these purchases will be tied to a single account, so only the free content will be easily available to an alternate account.