I don’t think certification standards differ too much. For the few domestic version Boeing does not make a new certification. More likely is that they certify a -400D with increased landing weight with tests made for -400. They then reduce the cycles from 25,000 to 12,000 and schedule a complete inspection/replacement of the landing gear after 12,000 cycles to prove the further usage of the aircraft. 12,000 cycles translate into 6 years of service for 6 cycles a day.
I don’t know how much cycles are OK for a B747, but I know that domestic usage is limited to less than 10 years for -400. Another possibility would be mixed use for long haul and short haul.
However, any -400D will find itself in the desert long before its “mates of the production line” arrive there.

That a 400D will be retired long before a standard 400 is not surprising and if anything expected with the high usage on short sectors.