I work lots with helping different customers adapt to their 'new' aircraft and find the comments in this thread to be spot on. Especially on the military side where the leap is often from rather 'well-worn' equipment to modern the old habits and 'we've always done it this way' mentality is hard to break.
We do a much better job these days of making sure that the Aircraft Procedures on the manufacturer's side are suitable for line operations, and there is a lot of thought put
into their implementation. I would say that 95% of customer ideas for SOPs that differ from the manufacturer's recommendations disappear after a good explanation as to why the system was designed that way. You know, those conversations that end in, 'Oh.....I didn't realise....' Certification has a much longer reach these days as well...
In any case, if you want a unique procedure then the best route is to obtain a letter of 'No Technical Objection' from the manufacturer through their publications department. This ensures that you're not impinging on any certification or technical standards of which you may not be aware and also won't void any repair/overhaul agreements. These requests get some technical oversight as well and I would recommend that you include at least an index to, if not a copy of, all No Tech Objection notices in your publications.