The problem with the Manual Payment is that it requires a lot of steps that may not be enforced, meaning that the participant will have to upload a payment receipt of some sort. Most users are not savvy enough to "print" to PDFs and email the file to the Manager (even if you have specific instructions!). They would copy and paste the result from the internet banking system. Some may pay at ATMs, which will force them to generate a scanned version of the printed receipt (although most have cell phones and laptops with cameras, they hardly think of those options also).
In any case, the Registration Manager won't have an easy task checking each payment to confirm, as this will have to be done individually.
Most events don't have enough people working to dedicate a single person to handle only registrations. And these events are shared, which means, they share the sponsors (not the day they happen), but registration is simultaneous, which becomes a bigger hassle.
Most of the payment methods require a lot of work. In Brazil, we have a PagSeguro
service (requires a business account with them), which is similar to PayPal, but allows credit card payments to be split in up to 12 months, bank bills or other 2 methods I don't remember now. They have a PHP script to add to any site, but they charge a pretty high fee for each transaction (lower than direct banking APIs, though). I'm not sure if it would fit the "late payment" requirements, we'd have to check.