Fire Drills - I am a lot happier when the RFM says 'Confirm Engine Fire' (AW139) than one that directs me to obey the light regardless (S76). It provides the opportunity for some options.
General - You may think that the Limitations section of the RFM is the only 'mandatory' section but you just try arguing your case when you are stuck in the witness box and one barrister after another asks if you think you know better than the bloke that designed and built it. Simply being in the right will cut little ice in front of people who do not understand the minutiae of our world.
If you want a good way out then put the checklist revision into your ops manual and get it 'accepted' (NAA will never 'approve' anything other than your FTL scheme and your tech log - in UK anyway). At least that way you can argue that your revision has been reviewed by a competent body.
G
PS. When I use the word 'competent' to describe the aviation authorities there is absolutely not one jot of sarcasm in my words, really.