That is not what Eccentric are doing. They have multi-acquirers. So if Frikkie has a merchant account at Standard Bank and at Nedbank, they will route Standard Bank cards to Standard and settle into the Standard merchant account, and Nedbank cards to Nedbank and settle into the Nedbank Merchant account. What the PSP will not do is interfere in the settlement path - i.e. if an ABSA card is presented, and the merchant doesn't have an ABSA merchant account, they will not route the auth to ABSA. However, its only a matter of time until they do.
In the bigger scheme of things, the path is quite simple : Merchant -> Merchant Acquirer > Card association Network -> Card issuer. The merchant acquirer is split into multiple roles, the two main being merchant account holder and payment processor. In this country, you will see examples of where the acquirers hold the merchant accounts (and the settlements and clearing that go with it) AND the payment processing (ie. some banks own the POS devices and the networks issued to the networks), and you will examples of where the payment processing is split out of the acquiring role (PSPs, host to host etc). In the US the border between the two is a lot more fluid than in SA because we are more legislated as to who can do what role. You still need to bear this in mind because when you hear companies like Apple talking about acquiring services, it doesn't necessarily mean the same as we interpret it - the merchant account holders and settlement. Often they are talking about the processing part. Apple do meet the US definition of a full acquirer though, because they do hold Merchant accounts for US Apple Pay merchants (when you register as a US based Apple Pay merchant you are issued with a merchant account for settlement). When we translate this back to SA though, Apple are not going to be able to do this part, they are only going to be able to do the payment processing and they are going to have to partner with the existing PSPs and Banks for merchant accounts and non NFC processing (what merchant will not want a POS device capable of accepting EMV - they are not going to rely solely on Apple Pay so will need additional merchant services). Hope this helps make it a bit clearer. I know you get it - this was for the benefit of everyone else wondering how it fits in. It is important to note however, that even though Apple are challenging in the Payment space, they are not "going after" the big three. They have partnered with them and are essentially also using their networks for card association interchanges. They just have a preference - in the US - to go directly to the issuer. How this will play out in the USA is that banks like Chase will be able to issue Chase cards without a license from the big three for specific use on the Apple Pay network. The advantage here is still under NDA, but from what i can gather, it all relates to Apples future vendor loyalty program (most bank loyalty programs are funded via swipe fees).
Strictly speaking, yes, you have to be a registered financial institution to be an acquirer if you are holding money/value at rest. Apple must be registered to hold value in accounts in South Africa (prepaid accounts, vouchers etc). I imagine that they have done that already, because they hold liability in Rand in the ZA store. I imagine they have partnered with a local bank or Financial Services Provider to do this, but I dont have the foggiest which one. I will dig and see what I can find out. 
And Yip, Masterpass is treated as Card present because of AMT.
