Graeme, I have now included a system of rating 'non-compliance' items to my commissionings. I highlight everything that doesn't comply precisely to the recommendations of BS but then highlight those 'which in my professional opinion are of no detriment to the proper operation of the system'. This might, for example, include a detector sited only 450mm rather than 500mm from a wall etc. etc.
It is the 'interested parties' responsibility, and not mine, to decide if strict compliance with the letter of BS recommendations is necessary, but I would hope my comments would give them the confidence not to insist on the designer/installer making loads of unneccesary minor adjustments.
However, the reason I highlight even the most minor of BS digressions is so no 'smart arse' later tries to insist I have missed something on my commissioning! No-one outwizzes the Wiz!
It is right that the training courses make it clear that everything should be checked carefully. If not, a major ommission might occur.
You should be able to prove that you checked everything by highlighting every problem, no matter how small. But you should also be able to point out which of those small problems are of no serious consequence.