Thrust,
I think this is a simple case of the tail wagging the dog. The Ref+50 is a new addition to the port page and was only added after it was realised that most, if not all, B744F crews were flying this profile to meet the "climb as rapidly as possible" requirement. Management elected to add it to the port page to ensure a standard is maintained. I guess it comes down to where you place your focus, to reduce thrust or to race towards 3000' for light traffic/noise. As Turtlenest wrongly alluded to, it is not to prevent metal crunching.
In N/A they use "TERPS" to design the criteria to build a departure. It requires 200'/NM climb rate for initial climb rates. If the departure required a greater climb rate it would be stated on the departure page with corresponding speeds/climb rates. Therefore, this requirement is for environmental reasons.
Normal T/O flap is 20. Obviously climb thrust can be selected at an earlier point by programming "the box" but it is defaulted to climb thrust at flap 5.