I thought it was very telling that out of the 136 companies surveyed, only 2 had a payment system. Speaks volumes about the sort of companies YC is trying to incubate/build.
Notice that both that showed up were intrusive payment systems. What I mean by "intrusive" is that they take you away from the site you are shopping on to enter your payment and shipping information on the payment system site. My guess is that this is the only kind of system the reporting site detects, because you can find it by noting the links to the payment system site.
If a site were using a transparent system, where the payment and shipping information are posted back to their own server and they deal with it on their own backend, it probably would not show up.
For instance, if your cart checkout just posts back to your PHP or Ruby code, and that code uses Braintree's PHP or Ruby API to process the payment through Braintree, there is no way the reporting site is going to know that you are using Braintree. Same if you are using Merchant e-Solutions, PayPal's PayFlow Pro, or something similar.