I did miss them. Sorry :(
A: When accepting Stripe payments via Snappy Checkout, all of your customer data is still available in Stripe. If you left Snappy Checkout to use something else, the only thing that would not work is subscriptions. I don't use Stripe's system for subscriptions -- that is all handled in Snappy Checkout. And, if it really proves to be insufficient, I'd like to make it work for you if possible.
A2: Snappy Checkout creates customers in Stripe's system. So, you could still charge existing customers if you found another 3rd party system that allowed that. I don't think it's possible to charge existing customers from Stripe's admin right now.
A3: Good question. I'm not sure though -- a possible import process maybe? I suppose that would be tough since Stripe/PayPal hold all of the credit card data. My goal is certainly not to push people away when a roadblock is encountered. I'd like to make Snappy Checkout work for anyone.
Correction: For existing Stripe customers, you can create new charges/subscriptions from the Stripe admin.