To be clear, things like you're describing are ok to tweak a bit, in my opinion. My airline however, has a tendency to change more consequential procedures- like flight control checks, go around call-outs and splitting of duties during critical phases. That kind of stuff, you shouldn't mess with, no matter how well it worked on the DC3.
The SMS folks should absolutely have a say in the SOPs for a given operation. As you said, different theatres present different challenges, but their recommendations shouldn't go contrary to the manufacturer's SOP.