I see no problem with using the Item of Power rules for this type of thing, but keep in mind powers need to be justified. I do not really like the idea of a familiar IoP that gives True Aim or Claws for example (unless you flavor your fists attacks/skill rolls as the familiar attacking for you), but I have no problem with it helping you with alertness/senses, because it can communicate with you. In order for this to work and be fair, it should be the same (mechanically speaking) as any other item of power.
So for the Cerberus Cub example, I see no problem with the character being able to use Pack Instincts/Echoes of the Beast/Ghost Speaker when his pet is around (with his own skills), and narratively describe it as the pet sensing/interacting and relaying this information to him like a translator (either by talking or some mental connection). When you get into combat, it gets a little weirder, but I see no problem with the character using his fists roll, at +1 for true aim, with weapon 2 for claws, and having the attack flavored as the Cub going and biting/mauling someone (in the character's zone). Mechanically this is the same as an item granting the character these powers, but the narrative flavor of a power or stunt can be whatever you can think of.
For the Malk, I personally do not get the flavor of the Malk granting refinements, but that is not really a necessary part of the "item" (the character could just take them, and the item would cost -3 with a +2 discount). Also, Malks do not have Glamours, but I do like the concept of the item of power granting magic being flavored as your pet actually doing the casting (using your skills of course).
As for the indestructible animal thing, since the character and his pet will generally be in the same zone (in combat), there should really be not a mechanical distinction between attacks on the character and the pet (by the rules any attack that could target the pet, could also target the player), so again it all just sues the players stress and consequences. Out of combat, I would likely allow the player to invoke his "Item of Power" related aspect for effect to have the pet go off exploring or whatever without him (still using his skills, plus any powers the pet grants). This does not seem OP, even if the pet cannot be hurt itself (at least to me).
Basically, if you use the IoP rules, the mechanical effect it grants should be the same as if the pet was actually an item granting the powers to the character. How you flavor that narratively is totally up to you. Further, since aspects are so fluid and story driven any way, such an "item" provides great justification for invokes that a normal item could not (and possibly compels when it gets "dog-napped" or something).
