I wonder if the 'gear down' dates back to the 767 first flight experience - when they retracted the gear on the 767 first flight the nose gear sheared a hydraulic line. They quickly put the gear back down before they lost that hydraulic system, but they flew the balance of the first flight with one hydraulic system inop (apparently they'd identified the nose gear issue prior to first flight, and installed a re-designed part - but the paperwork hadn't caught up and the new bracket was identified as a non-conformance and replaced with the original part prior to flight - oops
).
To elaborate a bit on what Pilot DAR posted - CPR basically says that anything that is being changed relative to the original cert basis needs to meet the latest regulation. There is precious little common between the original 777 and the 777X (new wing, engines, most avionics, even the fuselage structure has been changed) so it may not be a complete new cert to the latest regs, but it's close.