Just my two penn’orth here but while Boeing etc build aircraft but they don’t operate them in the airline environment. I remember chatting to a colleague who flew with a Boeing rep who was looking at the operation. The Boeing chap explained that while they set out a basic SOP the airlines, in consultation with the manufacturer, may elect to devise an alternative SOP that fits their operation. It’s a collaborative process not one party dictating to the other. For example, Boeing might specify the landing checklist to consist of gear and flaps only whereas the airline might add cabin secure, speedbrake armed, missed approach alt set etc.
I don’t doubt that the manufacturer has a lot of expertise and they get to see reports from various airlines but equally the airlines have real world experience not least when the pilots might be inexperienced, fatigued etc. SOPs vary from company to company because that’s human nature and different operators evolve differrent methods to do essentially the same job being getting from chocks off to chocks on in one piece!