There are at least 3 Houses in the Order with sufficient organization to make non-adversarial relationships the norm. If you are a Tremere, Guernicus or Mercere, you, your master and your filii are all part of something bigger, and are likely to remain that way for the rest of your life. And oddly enough, Bjornaer. Your master is likely to live for decades after he finished training you, and he probably has intentions beyond giving a PC an excuse to take Tormenting Master. You too are likely to live a long time, and when it is your turn to train an apprentice you are also likely to indoctrinate him.
Under AM2 rules, a magus looking to optimize himself should study from vis, because there is no other way. Under AM5 rules, a magus looking to optimize himself will use those resources to foster good writers, because studying from vis is far more expensive than under AM2 rules and because there is a much, much better way.
I think that AM5 is much better, on the whole, but many of the assumptions about balance and setting are based on that earlier setting and mechanics and have not really been recalibrated... hence YR7's and others' yearning for lower power.
For me, being asked to justify why NPCs get to do this really turns the issue on its head. It's like being told, "You need to answer why those barbarian overlords have managed to established complex societies that breeds unnaturally large horses and develops increasingly good steel weapons when they could just thwack each other with tree branches." It is certainly reasonable to play in a world where the technology is low, and barbarian overlords can self-justify it. But it's not the only or necessarily best way.
For me, everything you suggest boils down to, "D&D3/3.5/Pathfinder allows characters to create or buy magic items for sale or use, but these should be rare and never sold because I don't like the power escalation so let's create obstacles to make sure this doesn't happen." That's certainly a reasonable approach to play but it's a far cry from game mechanics that naturally support a world in which magic items are rare.
My way of seeing things is particular, not necessarily right, best or good. But one way I like to look at game rules is to try to optimize and see if the outcome matches the fluff, because I believe that people within a world tend to want to maximize their outcomes (though they won't all have the same idea of what is best; a man who is smart but lazy will optimize for relaxation. A Tremere elder will optimize for something else.) A match represents (one kind of) goodness.
One thing I dislike seeing is when the PCs do something that is obvious mechanically but against the fluff, so that all the NPCs look like incompetents.