practical calibration assumes the pinhole model for one specific arrangement of optical elements. if you move any of them, which happens if you change focus, the whole thing is all but a different lens. certainly, in practice, the focal length changes. slightly, if you’re lucky.
no. refocusing is worse than slightly out-of-focus images. because it changes the focal length, and due to reality, the distortion as well.
just make sure the lens is focused such that objects at the expected range of working distances are reasonably in focus.
“reasonably” meaning optical focus isn’t much more than one pixel’s worth of blur, or whatever you deem acceptable.
all of that is “conventional wisdom” I’d be surprised if it weren’t found in dusty text books, i.e. it would be a challenge for you to avoid reading about it. it almost seems as if you picked those things and negated them, challenging us to correct you.
or maybe my view of the subject matter is skewed by practice, and all of this isn’t talked about in literature? no, I don’t read books. they were merely supplementary to the lecture and exam.
I’ll see myself out again.