No. It is the rule explaining Magical Senses. So it describes what the rule covers. You are free to extend a rule with a house rule - but this violates the OP request.

And why would something like the Wise Owl of the Wood be more confused by a magical sense than an average person would be?
You find the answer in A&A p.31f The Human Mind:
The principle difference between the mind of an animal and that of a human is the possession of a soul, which is unique to rational beings such as humans, angels, and demons. The soul provides both reason (ratio) and intellect (intellectus). Reason is exercised when one proceeds step by step to prove a
truth that is not self-evident, and is the highest function of the cognition working in conjunction with the soul. Reason uses the input from all the inner wits — the sensory species composited in the common sense, the unsensed impressions of the estimation, the memory of past events, and the imaginative powers of the cognition — to reach a conclusion that none of the individual parts of the mind is capable of reaching alone.
IOW: The owl does not understand, that its senses have been altered. It does also not understand, why its senses now show weird stuff, and what this weird stuff means.
This is different for an owl familiar with Intelligence instead of Cunning: this is a person with reason, to whom the spell caster can explain the effect of the spell.