To what extent can the original manufacturer's checklists be altered
Be careful. I don't know about the smaller aircraft types but checklists for larger types such as jet transports have been carefully crafted by the manufacturer taking into account (for example) recommendations from previous accidents where checklist design was a factor.
There are a host of other factors to be considered before fiddling with the original manufacturer's checklist items simply to suit the personal preference of company management pilots.