Serf's Parma on these answers, as I'm basically going by memory...
Only those applicable to the focus, but I think they make them stressful and supernatural as well. Also they add botch dice, and remember to watch for 0s and 1s when they're active. I suggest interpreting their applicability extremely broadly, because they don't happen all that often.
I don't think there's a specific mechanism for getting them through play; if you don't have the Virtue you don't have the Trait. You can get one temporarily by tinting auras, and maybe after a while it would become permanent. If a character's vitality is constantly preyed upon by a faerie or he gets lots of Warping from the realm, I think giving him a point of positive Sympathy is appropriate. If he gains lots of cool new faerie stuff, it might make sense to balance him out a little with a negative Sympathy Trait, too.
The impression I got from reading was that the penalty only applies within the focus, but the botch dice are for any time you stress roll, and the 'reason' for the botch ends up being thematically related to the sympathy that caused it. So... say you have Rocks -3 as a Sympathy trait. If that causes you to botch in combat, the reason for the botch is that you tripped on a rock, or something.
I was, in fact, referring to the Botch dice when I said "penalize", but I got my answer anyway. It does seem awfully harsh though, perhaps negative Symapthy Traits are rarer than I thought at theast it provides an incentive for characters with high negative traits to buy them off.
I now have another question though, this one concerning Faerie Rank.
All of the examples imply the character that the character's highest trait will be positive and his lowest trait negative, what if this is not the case?