Let me start by stating that I don't think this happens.
But ... here's the incentives as I see them, all of which would kind of have to exist for this to even potentially work.
1) Jerry Jones believes McFadden will bring him a Super Bowl ring ... or two.
2) McFadden's agent realizes that he's not even going to sniff the top 5 and could freefall as far as #13 overall. With that in mind, settling for #3 money and being selected by a Super Bowl contender and having the distinction of the #1 overall pick AND being seen as "not about the money" sure would look appealing.
3) Parcells & Co. like the package of picks + player(s) being offered.
That's it really, each of those are major things, but those are the only things. Nobody believes the draft value chart is valid anymore, and everyone involved realizes this draft isn't the type where the top pick is a special one.
Jones stands to land 2 very good football players with his 2 first rounders, and while the 2nd day picks aren't nearly as crucial for him, there's a lot to be said for picks that could net you guys like Quinton Groves, Jeff Otah, Aqib Talib or Felix Jones among many possibilities at 22 and 27.
For McFadden, the closer we get to Draft Day, the more he is going to realize that none of the teams picking in the top 5 can really take advantage of him right now. Pre-Negotiating the contract prevents a holdout, and makes perfect sense for McFadden.
This makes a lot of sense for the Dolphins, who want and need to stockpile draft picks and young players. Forget about who the player might be for a moment, think about the 3 draft picks. With the 4th rounder we could still potentially get a starter, and the two first rounders might be Brohm, Connor, or one of the guys previously mentioned. Any way you slice it that's 2 to 3 solid starters. Parcells isn't necessarily great at building a Super Bowl winning dynasty, but he is good at quickly building a playoff team, so he'd get closer to that goal with 2 first rounders than 1.
Still, I don't see Jones pulling the trigger as he'd be the biggest loser in this scenario really. And this sort of depends upon McFadden's agent convincing him that he's NOT going to be a top 5 draft pick, and agents almost universally blow smoke up people's ... well you get my drift, they tell them they're better than they are so they don't get fired and replaced by another agent who tells the kid they can get him top 5 money. I definitely think the Dolphins would make this deal, as well they should if this offer ever really were on the negotiating table.