THINKING as opposed to being an FOM/POH/AFM junkie
Such documents definitely should be read with commonsense and a modicum of intelligence.
Indeed, I can recall the then Head of Certification in the local Regulator observing that one didn't necessarily need to observe the documents .. with the caveat that one might then be called upon by the Regulator, insurer, or the legal system to demonstrate compliance with the Certification etc. requirements for the "non-compliance(s)".
That is to say, "thinking" is eminently admirable and to be commended .. but make sure that it is backed up by a LOT of knowledge if you intend to go it alone. Even where the commander exercises command prerogative ... he/she may have to justify the decision to go outside the rules with considerable risk of penalty if the story is not up to speed ...
For instance, looking at the POH side of things, I routinely conducted takeoffs with zero flap in light twins when the POH/AFM didn't contain data for that configuration. However, I had done my own reasonable and conservative calculations backed up by some simple flight tests to confirm the sums .. the Regulator's folks (both Certification and Flying Operations) never once queried my approach to the matter ..
One of the benefits of complying with the published requirements is that you are then placed rather strongly to argue the point after the fact ..