Isn't the point that some bidders will not know which it is when they make the bid?

RTB bid requests have support for the normal auction based bids but also indicating possible private marketplaces which may come into play depending on the exchange and seller, meaning that the highest bidder will have indicated to the world their price, but not won the auction, so they may (erroneously) conclude next time to try bidding higher, leading to price distortions.

I suspect a large proportion of advertisers still believe the whole thing is a nice transparent fair auction process, and have no idea of how convoluted it has become.

They do know if the bid is part of a PMP. They can still place an Open Market bid if allowed but they should reduce their expectation of winning that auction, even if they're the highest bidder not because of skullduggery but because the publisher has a prior arrangement with a DSP or advertiser.

Valuing a bid is a complex and interesting task. Ever since Second Price auctions started dying out DSPs should have moved to essentially algorithmic trading. A price calculation depends on tens if not hundreds of factors that are evaluted on a per auction basis.

Advertisers have been demanding more transparency into where their money is going for quite some time now. If you're an advertiser and your DSP isn't giving you detailed reporting into the fees they're being charged then it's time to move DSP.