In what way were you asking?
You count as your full class level in terms of what it does.
In terms of things that have class stacking with it like familiar or animal companion levels I can see where that would be a problem. In which case I'd rule that they do not take anything over your character level as the intent was to allow you to go crazy multiclassing while allowing you to retain a few key abilities to help define the character more.
I will say though that with Boon Companion jack of all trades isn't a particularly good feat to use for that purpose.
Also, I was the one who wrote that feat so take that straight from the horses mouth as it were.
I was more just wondering about Eidolons or the like but yes only to the limits of character level regardless sources.