What does it mean that they gain an extra opportunity to put a rank in Skullduggery, Vigilance, and Knowledge? The latter section on spending skill points makes it clear that race/career bonuses don't let anyone increase about a skill rank of two starting out. So what is the "extra opportunity"?

They use fairly inconsitent wording, but I read it as a convoluted way of saying that you can effectively double up on the free ranks from both the broader smuggler career, and the theif specialization into the same skill (note that vigilance, skullduggery, and Knowledge(Underworld) are overlapped with the thief).

Basically:

Every career has a general set of skills. A player character may choose 4 of them to have +1 rank.

Every Specialization has a smaller set of skills (note that these can overlap with the career skills). A player character may choose 2 of them to have +1 rank.

A player character may opt to add 1 rank to the same skill if it is contained in both the career and specialization.

A player character still cannot begin play with more than 2 ranks in a skill.

Thanks that was what I was thinking, but the text indicating that such bonuses made the Thief the best at those specific skills when starting out didn't mesh up with that. Anyone can take 2.

Hm, that's not exactly proofreading feedback, any tips on the best forum or thread to comment on that wording? It sounds like you likely already have, but I'm not finding a thread from searching.

The point is that there is not extra cost incurred though. If you can stack a career skills/species skill/specialization skill, you basically can get a free 5xp out of the system.

Still, it needs to be noted that it caps at 2 ranks.

Its annoying because they really could just put this wording in a single spot.