I agree with the OP that a FAQ entry is needed to clarify how this should work. It's even more of a mess when we look at the Skirmisher entry and contemplate what it might mean for the AnC to learn "hunter’s tricks from the skirmisher ranger archetype instead of standard tricks." Aside from the questions already raised about when this ability begins and how often it can be used, it's not at all clear how the skirmisher's tricks work when they are done by an AnC.
In particular, for the purposes of this ability of the Hunter class, in the text of the skirmisher's tricks, should the words "the ranger" be replaced by "the hunter's animal companion"? That would work pretty straight forwardly for some of the tricks. For example, the very first skirmisher trick listed "Aiding Attack" - if an AnC with this trick hits an enemy, the next ally who also attacks the same enemy gets a +2. Ok, simple and no problem. Similarly, "Defensive Bow Stance" would give the AnC the ability to make ranged attacks without provoking AoO; since most (all?) AnC won't have ranged attacks, this trick would be legal but irrelevant for them.
But what about tricks like "Ranger's Counsel"? If there are no limits on how often an AnC can do these tricks, can I instruct my AnC to have Ranger's Counsel (Perception) perpetually turned on, thereby giving everyone in the party a continuing +2 Perception bump? Similarly, can I give my AnC 1 rank in UMD (once I bump his intelligence to 3 at level 4) and thereby use Ranger's Counsel (UMD) to have him give everyone in the party a +2 UMD whenever needed?
And what about the skirmisher tricks that specifically mention an animal companion, like "Bolster Companion," "Heel," and "Sic 'Em"? If we simply replace "the ranger" with "the hunter's animal companion" in the text of these tricks, they no longer make any sense at all (e.g. "The AnC can use this trick as an immediate action when his AnC is hit...") It can't have been the intention to make these tricks unplayable for Hunters and their AnCs, so some kind of FAQ explanation is needed.
One possible solution, but it's clunky: for those skirmisher's tricks that explicitly reference an AnC, the text should be read as "ranger/skirmisher" = "hunter" and "AnC" = "AnC." For those skirmisher's tricks that don't mention an AnC, the text should be read as "ranger/skirmisher" = "AnC."
Even with this interpretation, the ability is still a mess. If the tricks are options that can replace the standard tricks, as the RAW says, what's the Handle Animal DC for them? The standard tricks all list Handle Animal DCs, which can help prevent an AnC from being trained in the most powerful of tricks at the lowest levels.
And how many of these tricks can an AnC have? By RAW, it looks like my first level Hunter could train his AnC in 7 of these tricks, even though a Skirmisher Ranger gets none until level 5 and will have only 4 of them at level 11. By contrast, an 11th level Hunter who bumped his AnC's INT at level 4 and 8 would have an AnC with 16 tricks (3*4 for INT, plus 4 bonus). Which makes the question of whether there is any limit to how often these tricks can be done even more pressing.
It's a mess. Hopefully we can get a FAQ ruling.