The Permanent Talents thing is a little confusing. It is only addressed in one paragraph on p.88 under Talent Trees (where they aren't even described with a term, merely as "marked with a red light"). The actual mechanics (you don't lose the ability to use these Talents if you abandon the Talent Tree you earned them in) are easy enough to understand, but difficult to find.
Further, on the Talent Trees themselves, the same Talent will vary whether or not it has such a Permanent red tag with no obvious rhyme or reason.
It is also not addressed whether or not a PC loses the lower purchasing cost of the Career Skills associated with a discarded Specialization. A min-maxing player would quickly note the value of purchasing and discarding a Specialization early on just to get a future discount on the 4 Skills associated with it. The cost is made up in just 2 Skill Rank advancements, even if it was an out of Career Specialization.
What if someone returns to a Specialization they once discarded? Do they have to buy back all the Talents they once had? what about the Permanent ones -- clearly they can't benefit from buying them a second time? These are clearly unusual cases, but they should be considered.
Finally, on p. 65 in the final paragraph of Acquiring New Specializations, the paranthetical note about where the three Specializations limit comes from is confusing, unnecessary, and reads more as a philosophical design explanation than actual rules content during character creation.