I was thinking that way too but here are my concerns:
1. Construction wise, I think you will have some hard time to make the male peg on the hand to go through the wrist plate on lower arm armor, then you have to make sure the male peg go through the wrist plate on valkyrie arm. It would be easier if you drill larger hole on the wrist plate to make more room, but bear in mind that the wrist plate in the valkyrie is rotating when you put the lower arm armor on because you actually can't hold it when you dress it up with armor. This is the main reason, I assume, that Yamato do the other way around.
2. Perpestive wise on toy value, ruining a mechanical hands seems doing less damage to the toy and I can reverse engineer back on the hands by inserting another male peg. Furthermore, the hands are optional parts which is not the main portion of the toy.
3. Customize the gbp-1s armoer seems doing more damage to the toy because it is one of major parts of the toy, many, like me, will hesistate to do so because it depreciate the toy with custom work on it and not keeping the toy "intact".