As a starting point SOPs/Checklists set down by the manufacturer should be adhered to; this if nothing else gives legal protection. The problem starts when these are added to or changed by various fleet managers without reference to the manufacturer or other operators. Boeing instructor pilots are continually amazed how different airlines can fly standard Boeing products in completely different ways.
On a lighter note, I have a theory that changes are only made to standard procedures as the result of a stuff up by a management pilot!