Bear in mind that chronotypes, as stated in the wiki, only varies about 2-3 hours from each other. This is just to say that there is no nocturnal person in terms of biology, we are all diurnal mammals after all.
I am saying out of the top of my mind but I would guess that in the case of owls they have evolved to be nocturnal. So their physiology is problably synchronized to natural light but in way that keep their activity nocturnal.
Hamsters are also nocturnal but you can force them to be diurnal in lab settings, but their physiology is at a constant jet lag state.