If you want to go really paranoid, assume that the demonic corruption of the Order of Hermes is very strong, and demons have managed to pass on their soul handling techniques to Hermetic Magic.
By giving an Animal an Intelligence score, you have to give it the capacity to hold a soul. Once it has the capacity to hold a soul, it can give a home to the first passing free soul (not protected by Might), igniting the Intelligence.
< eerie music >Of course, that free soul from a recently dead person will have it's journey to its final destination interrupted, be it Heaven or Hell. </eerie music>
Or, the capacity to hold a soul is also the capacity to be possessed by an angelic or demonic entity. Maybe some of the Infernal & Divine ways of manipulating souls (both exactly the same, really) have been passed into Hermetic Magic by Infernal agents; either as part of the Divine Plan or an Infernal intrigue... but the knowledge is incomplete. Right now there is no reliable way to divine anything about a soul, or even detect the presence of a soul, outside of various (rather unreliable) summoning techniques.
I tend to side with the 'significant number of mages' who think the failure to raise the dead is merely a flaw in current Hermetic Theory.
I don't wish to get involved in the discussion of the soul in the various rule books of Ars here.
They appear to be deliberately unprecise, because in the earlier 13th century a serious and momentous discussion in the Latin Church and the budding universities of the time was held about the soul and its nature. It led to a redefinition of its meaning, starting from its usage by the Church Fathers, proceeding over the reception of Averroes and Aristotle to the Summa Theologica of Thomas Aquinas.
Some of that discussion is used as a background in Sub Rosa 20 FRANCISCAN DOUBTS and Sub Rosa 22 DE ANIMA, which can be used as an Ars saga metaplot leading to a transformation of Ars cosmology.
The basic issue is, that man's soul is just an Aristotelean form of man's body, but for Averroes and Thomas is immortal as it has an intellect.
Something having the Int characteristic in Ars would not the other way around need to have an immortal soul.
The rules at least twice say mundane beasts with Intelligence don't exist (both HOH:MC p.38 and Book of Mundane Beasts, p.1: "mundane beasts have a Characteristic called Cunning in place of an Intelligence score.").
And spells that create magical creatures and faeries are already explicitly covered by a line in The Limit of the Soul -- "there are spells that appear to create them, but some magi believe that such spells really summon existing beings."
Well, am the player in Loke's Saga that asked about Elemental as Familiar. My Magus has the Elemental Magic virtue, and it felt more appropriate for him to get an Elemental as a Familiar than a magical animal.
And since he has affinity with Auram, he'd probably want to find and befriend an Air Elemental.
But in a more general sense, Magi do strange things if it suits their focus/direction. Some seek immortality, some seek other bizzare things like a connection with their Heartbeast, or other esoteric magic.