Well I think the reason is that the 5.45x39 is an approximately 50-57 grain bullet (normal circumstances) moving at 2800-3000fps. Equaling about 990-1075 foot pounds energy.
The 7.62x39 is a 123-154 grain bullet moving at 2400-2600 feet per second. This equals about 1500-1800 foot pounds energy.
So, I would interpret it like this. The weight of the bullet is key here. A lighter bullet (even when moving very fast) loses more energy both when moving and on impact, it doesnt retain energy like a heavier bullet would. The 5.45 will penetrate armor, but not like the 7.62x39 will because it has such a light bullet. The 7.62x39 has much less speed, but the heavy bullet retains more energy and will be more reliable when "punching through" armor.
Well then, that's my interpretation... Remember, we're talking about miltary grade body armor here (not accounting for ceramic plates), but if we were talking about low-grade armor that can only fend off basic pistol cartridges (.380, 9mm, .40, .45) then 5.45x39 will have no problems punching through.