A char when made can only have 35 bp of positive qualities, Does also count against qualities bought during game play as well?

During gameplay you can go to town with your Karma and buy positive qualities all you want, afaik, until the GM tells you to cut it out. The 35 BPs are only for chargen.

The GM however may not let you get the qualities you want. Especially if there isn't a special reason to do so (for example after a couple splatterfest adventures and having managed some torture I'd probably let my players pick up the guts quality).

For game balance I'd probably let a mundane hacker pick up codeslinger qualities.

I let people pick up any qualities that make sense for their character. As a general rule, it should either fit your character concept or have a reasonable in-game justification.

Magicians and TMs at the very least need to start with Latent Awakening/Emergence to buy those up later. Through extensive in-game efforts (or disasters), I'd allow a magician or TM to acquire things like Aspected, Mentor, etc. after character creation, but its hasn't come up.

I still haven't sunk my teeth into Runner's Companion yet, but from what I've heard, I may have to put some restrictions on some of those qualities.

-paws