Can an animal companion with 3 Intelligence — and therefore not limited in the choice of skills or feats — take Item Mastery feats in order to channel magic items using Fortitude?
I think the answer is "probably no."
Paizo have issued at least two FAQs on the subject:
The first one that I can think of states that "An Intelligence of 3 does not grant animals sentience; the ability to use weapons, shield, or tools; speak a language (although they may understand a language with a rank in Linguistics, this does does not grant literacy); or activate magic devices."
The second one states that "Companion creatures ... with an Intelligence score of 3 or higher can activate ioun stones," but that "Animal, plant, or vermin companions cannot wield weapons or activate magic items."
With that, you should also consider that using an item mastery feat is stated as being "similar to activating a command word item."
That's before we get to the larger conversation on the difference between an animal companion with an unusually high intelligence and an actually sentient creature--and there have been both Paizo blogs and developer posts on these fora on that topic.
But it's also worth considering that those are Pathfinder Society FAQs, and that while Jason Bulmahn, etc., have qualified that a remarkably smart animal is still "just" an animal and does not possess human-like sentience (and, importantly, they distinguish between animals with Int scores of 3+ and animals that had the spell Awaken cast on them, or magical beasts), the same developers have repeatedly and consistently urged people on here to not feel limited by either the rules or their positions on the rules.