Assuming the deal really was 25 million euros (I'm still not sure of it, there may be other players involved, there maybe extra values, etc - until the Portuguese stock market confirms it officially I'm not sure) it doesn't mean Benfica is rolling the carpet to Real.
Quoted values of 40 million were his clause, and Benfica trying to inflate his value the best he could, naturally says players only go out by the clause. Everyone does that around here, doesn't mean it's what really happens in the end. Di María has been obsessed with Real since the first rumors and was pressing hard to leave. Benfica needs to sell because they invested massively last couple of seasons and need some financial return. They just waited how long they could. If Real had given up on him and Manchester United now approached Benfica with 25 million euros you'd probably take him as well, assuming the player would be interested - and he would.
It's just business, if you go ask for Cardozo they'll say he costs 45 but in the end you'll get him for 20. Porto said no one would take Quaresma by less than 40 million, but in the end he went for 25 (of which 6 were in the form of a player that's not worth even 1).
If anything, unlike you say, people try to milk Real because they know they pay whatever it takes to have they players they want. On this particular case, it's complex, Benfica has a few former Real players, there is a chance that Real will loan them someone else, etc... I doubt there are any "preferences" other than these, which are very natural.