The
large payment security fee 
appears to simply be a ploy to work around the fact that VISA's rules only permit flat fee convenience charges (with an exception for tax payments).
See this document:
http://usa.visa.com/download/merchan...tions-main.pdf
...and search for rule: 5.2.E
As I read the rule they wouldn't be permitted to charge any fee:
The requirement for an alternate payment channel means that Mail/Telephone Order and Electronic Commerce Merchants whose payment channels are exclusively non-face-to-face may not impose a Convenience Fee., but that's probably been discussed elsewhere.
ChargeSmart offers variable fees in step 1 for some vendors, such as Lexus Financial Services ($16.40 for $500, $27.85 for $1000). Maybe establishing a credit card bill payment service like chargesmart might require a specially negotiated merchant contract, or maybe the fact that chargesmart is not the seller who originally contracted with the buyer makes a difference.
Anyhow, I have downloaded and at least glanced at the document you refer to, as it looks like a great reference to have for many other situations. Thank you!