Good point. Hypothetically, I'm asking the GM to turn a blind eye to the PC's bad reputation, and the player's lousy real world social skills.
One adjustment might be that as you say, the players aren't trustworthy. So perhaps the NPC, who needs the deal to work out, focuses on preventing or being prepared for a double-cross. In which case, if the deal goes through, great.
Thieves are used to working with thieves. That's not really the problem. The problem is that setting up this situation where negotiation is favorable to both parties when both parties are basically ruthless is difficult. And looking at it another way:
step 1: The villain isn't disgustingly evil.
step 2: The villain isn't looking to double cross the PC's.
step 3: The villain has an honorable reputation.
step 4: The villain opens up peaceful relations with the PC's.
step 5: The villain is clearly powerful and capable and not a push over.
The problem in this scenario is the players tend to make the determination: "This guy isn't a villain. This guy is an ally! And this guy is great! We can totally trust this guy! He's so cool. He's got poison. He's not afraid to torture people for information. He employs assassins. There is totally nothing that can go wrong here."
This leaves me as a DM in another bind. First, if the PC's later discover, "Wait, Master Blackguard knows so much about the villain because Master Blackguard is a slaver that steals children and supplies them to the very demonic cult we've been fighting! I never saw that coming! He was so Sauvé! He had panache! He offered us loot!", there is a tendency to treat this as betrayal on the NPC's part: "We've totally been had. I thought this was the cool sort of evil person, but really he's loathsome greedy man that would sale his own grandmother if the price was right! He's totally been working with the bad guys all along! We're totally going to ambush and kill him!" It rarely occurs to them that Master Blackgaurd, despite his comparative lack of morals, is negotiating in part because his own dealings are starting to sicken him and he thinks maybe the other villain is really beyond the pale, and after discovering he's really 'guilty' there tends to be a tendency for the PC's to cease to negotiate in good faith much less adopt some really advanced technique like trying to needle the villain's own atrophied conscious further.
But if on the other hand the character is all the above and really has no foibles worse than the fact he's cheating the imperial tax collectors regarding the pistachio tariff, there is a tendency for the 'villain' here to probably be more sparkling clean and decent than the PC's tend to be with the ultimate result that I'm not really convinced that if this really is a villain negotiation, it certainly won't be the player's that see it that way.
Fundamentally the problem tends to be that most players find anti-heroes and anti-villains more glamorous than heroes, and that comes out both in how most players play their PC's, and what NPC's most players will admire and desire to associate with.