I like your name! Devil's avocado!
As the PP said, it depends on your objectives. What is the point of this audit? To improve standards? To check compliance to your boss' idea of good practice?
Personally I do stray from checklists when I audit but that's only where straying from the checklist helps achieve an overall aim for example to make safe food. So, if I was conducting an audit on pest control but saw a personal hygiene issue, I wouldn't ignore it. That said, if there isn't management commitment in improving GMP standards, even if you do stray from this checklist, you may not have support in improving things.
I suggest therefore, you go back to your manager, ask him his motivations; perhaps suggest a few extra items on the checklist, don't go mad, if you're trying to improve matters, it's often easier to do things in small steps. Then, once you've audited and got that in place for a while, perhaps you could suggest some accreditation to help guide you improve?
In the meantime though I'd stick to legally required stuff as that's non negotiable. Presumably you are audited by government inspectors occasionally? What do they look for? At a guess I would suggest general personal hygiene (are people wearing appropriate clothing and washing hands?) provision of equipment to ensure food safety (e.g. handwash sinks in appropriate places) and temperature control (cooking and chilling).