I don't think it's necessarily antagonistic. Rather it's just a common sense approach. The GM is expected to spend PP on "bad stuff" happening. The players know this. Therefore, when spending a PP that will be given to the GM, the ultimate "positive benefit" of that PP should be taken as being "good stuff it adds - bad stuff it causes". This is true no matter what the relationship between the players and their GM is. Players who understand this can start feeling like spending PP is meaningless and be less excited about doing so. Ultimately, the GM doesn't need PP to create interesting problems, he just throws them at you. Like he does in every other P&P game. What the GM needs PP for is to "break the rules", make NPCs take a double movement, make them use the "Revenge" plot power when they're hit, and so on.
For point #2: The GM doesn't care if some NPC gets pummeled because he gave the PC a plot point. He certainly doesn't care that (or rather, he likes it when) a player spends a Plot Point to add an interesting narrative detail to the story that is of benefit to the PCs. Therefore GM generosity shouldn't be affected, unless he is indeed an adversarial GM.
Worth noting that the game "Fate" has used a system like this with its Fate Points for years now, and it works fine. The exact numbers could be tweaked a bit, and a mechanic could be in place to give a GM more plot points (in Fate, making NPCs concede a combat early gives the GM more Fate points in the next scene, for instance). I hadn't thought about all the Plot Point generation powers yet, perhaps PP equal to twice # of players would be better. I never considered that Plot Points generated by amps would be given to the GM though, that's why I thought they were called "bonus" plot points. Seems a bit weird to spend karma on points that will end up in the hands of some NPC after you use them.