Dik et al, there is no problem with the way certification authoritiesdeal with change. The process is addressed in part 21.101 - called the 'changed product rule', and provides pragmatic criteria for the identification of the appropriate cert basis for modifications to existing designs, i.e. work to the latest amendment for 'major' design changes.
If you look at the 737 tcds you will see the cert basis becomes incrrasingly complex with each generation, as various new amendments become applicable to the incrementally changed systems/structures.
Furthermore the regulator & applicant can agree upon special conditions where the basic regulations are deemed inadequate for specific novel design features, which is the case for just about every contemporary aircraft type.
It's a misconception that 737ng/max are designed entirely to 1960s design standards.