I may be missing some technical issue, but would it not be better to just take a cut from the sale as it is purchased? It seems round about for me to have someone purchase something from my shop, the payment then be processed through paypal, which then is deposited in my bank account and then the commission charged from the account. Maybe there is no way to do that with PayPal?
If we would take money from your customers directly we would be liable for your wears. This might be ok in 99% of the cases but what if someone sells a liver?
Also this way our customers aren’t forced to use any particular services. Shopify works well in an existing infrastructure with already existing paypal, authorize.net accounts and so on. Think of the bill as something like the phone bill at the end of the month…