Really don't understand why an airline would want to deviate from the manufactures recommendations.
Airlines have flown billions of hours in manufacturer's products. Boeing I would guess have flown thousands of hours in comparison. Manufacturers are reluctant to make any changes to their initial operating manuals unless there is a significant safety case to address. They have recognised we live in a litigious society and are massively protective of their own procedures, mainly because that's what went in to print when they launched the aeroplane. Boeing in particular have a very "it's up to you, Jack" approach when giving guidance on how to fly their products. To introduce further rule would leave them exposed to finger pointing and law suits. Hence they put the onus on the pilot to use his best judgement, thus carry the can should something go wrong.
Airlines however are overseen by their local country's governing aviation authority. That authority must approve any change to the airline's procedures which differ from the manufacturer's. As accidents occur over the years, loopholes in operating procedures are closed up by way of adjustment of an airline's SOPs in an attempt to prevent the accident/incident re-occuring. Authorities conduct 6 monthly audits of airlines to ensure their Safety Management System, alongside other Flight Operations Departments, is up to speed with latest safety risks and is doing something about minimising them. Manufacturer's don't do audits on how airlines are flying their aeroplanes. To their mind, once you've bought it, it's up to you how you fly it! (..save for instance the QRH edition change for the 737 some years ago.)
A classic example of manufacturer's approach to standards in comparison to an airline's is the autothrottle function on the B737 manually flown approach. Boeing in its FCTM says disconnect it. Conscientious airlines recognise there is a loophole here that the TOGA thrust function is now lost. Airlines recognise the go-around phase as one of increased workload, thus many promote the use of leaving the A/T in ARM with the SPEED function deselected. This affords the facility of manual throttle, with go-around thrust setting protection. There is a definite safety case for this. How could one possibly argue that complete disconnection of the system is safer? Or is it the preference of care-free pilots to show off their "straight arm" technique on a Go Around as they light a Hamlet cigar?