I came up with the effect first, liked it, and now I'm trying to come up with an explanation.
In this case, the armor's increased defense comes from different focus. This only applies on Jomonese, not Japanese, armors, but I imagine the the armor would be designed so it doesn't hinder the usage of the samurai's preferred weapon. Samurai Armor + broadsword/buckler equals defense penalty, but Samurai Armor + katana does not. Other nations' armor isn't as specialized, because some use swords, others use morningstars, some only use spears, they use different shields etc etc.