Its basically impossible for an OEM to "wash their hands" of any responsibility, no matter what they do. Even if a crew were to go against every single procedure in the book, you'd find someone trying on the "but they should have catered for this anyway" line.
What the NTO is doing is basically saying "the OEM disagrees that this is the best procedure, but it won't in itself break the systems". Since this company-specific procedure is presumably covered by the company SOPs and approved by the local airworthiness authority through that route, the crew are hardly 'on their own' in any case.