The new errata answers the question clearly:
Change to following sentence: “You get a free Power Point whenever you
increase your Magic attribute, and you can gain a Power Point through
Initiation (p. 324) instead of gaining a metamagic.” To: “If you’re an
adept, you get a free Power Point whenever you increase your Magic
attribute (though this doesn’t apply to mystic adepts, and you can
gain a Power Point through Initiation (p. 324) instead of gaining a
metamagic.”
Therefore, further power points do not require spending of karma, but do require to forfeit a metamagic when initiating, and can only be acquired by initiation.
First, no. There is no good, hard rules on adding negative qualities during game. There have been suggestions and precedence that have been set by Addiction rules. But, for the most part, it's up to the ST. Because of this, I can't really give you a RAW explanation of what to do.
However, I CAN give you better on your second question.
I've had a number of games in my campaigns where I've added negative qualities for things that players have done during the game. A few times, it was addictions. But one of them was an Enemy. During the game, the runners had been sent against a corp executive that had some information for their actual run. While doing the run, one of the players thought it would be a good idea to blackmail him. I had let the player know that this guy was a pretty high-up executive and blackmail wouldn't go over well. However, they continued on with their plan. It had succeeded, since he had a good idea about it. However, the blackmail data had been caught by a rival group that wanted to deface the exec. In short, there was a fire fight and some fun with jumping over moving cars. In the end, one of the group had gotten away with the blackmail data before the runners could give it back to the exec and the exec escaped.
Now, the one that had been doing most of the blackmailing and talking has a corp executive with a lot of resources wanting him dead. What does this mean? No more taking runs from this corp...and sometimes, they would have to deal with a group of runners or corp security as a distraction during other runs.
The player liked the idea and took the negative quality. And, after a while of having runs sometimes go pear-shaped because of a group of newbies wanting to cash in on the bounty on the one runner, he finally paid up on the negative quality and I gave him the chance to eliminate the exec.
In short, negative qualities are something that you can add to players that will give them different hurdles for doing things half-assed or screwing up. And you still give them the ability to use Karma to buy the negative quality away. But I wouldn't constantly do it. Once ever three games, and only when they really deserve it, seems fine. It's not so much that it would make the game more gritty. It just makes it kind of unrealistic to carry around that much negative baggage. If they earn it, they earn it. But I wouldn't slam with it too much. And you shouldn't reward them with Karma or give them more for giving them the negative quality. They earned it from doing whatever got them the quality.
Best Answer
The quoted sentence places no restriction on its benefit, and says nothing about initiation. It should apply as of character creation. Following your interpretation, a mystic adept with magician's way would have access to the metamagics immediately, and should use initiation for other purposes.
However, "free use of all regular metamagics" is a very powerful feature that people would talk about in online discussion forums. They don't. It's also problematic from a game balance perspective. Should a character instantly become more capable whenever you buy a splatbook?
Therefore, logic indicates that the RAW phrase "have access to" means RAI "are allowed to purchase". When the sentence is viewed as a redundant restriction on physical adepts, the rules are consistent, although worded poorly.
Update
Reading the section on Ways more closely, I note two things:
p.s. An alternate interpretation of the sentence is that Magician's Way adepts are allowed to poach metamagics from the various Schools without having to be a member (i.e. if you enforce "These metamagics are only available to those who initiate into this school of magic" from p.139).