The Proceedings of the National Academy of Sciences has an interesting manuscript submission process.
Apart from allowing NAS members to "contribute" a paper from their own lab that they've gotten peer-reviewed themselves, there is a curious distinction for more normal submissions.
The pre-arranged editor track permits you to find a PNAS editor before you submit it. Presumably a friendly editor.
In the best case it is similar to a pre-submission inquiry practiced formally or informally at the GlamourMags. In the worst case, an end run around "pure" peer-review via the Insider's Club.
(The end run being as benign as simply avoiding the desk-reject and as pernicious as getting a gamed peer-review.)
But is this any different from other journals? GlamourEditors require some buttering up. They brag in unguarded moments about how much they've "worked with" the authors to make the paper awesome. So many of those papers end up functionally identical to having a pre-arranged editor who has agreed to handle the manuscript.
In pedestrian-journal land, one can easily go Editor hunting. If a host of journals sort-of fit, and the IFs are indistinguishable, then it behooves the authors to seek a journal with a friendly Associate Editor. And to ask for that person in the many submission systems that permit such requests.
So really, how does the PNAS system really differ?
In fact, you might see that as being more honest and transparent.