Would be a hilarious outlier for Snake to scale to something like 1000x above stuff that can consistently cripple or kill him. I mean the very feat Vamp scales off, is something that was depicted as being fatal for snake. Even later, ocelot punches outer heaven, dents it, with a dent about 500x smaller than Raiden's dent. Said punch he used wasn't held back and hurts snake, if hits. that also begs the question, does Vamp ever actually hit snake canonically? or even raiden in 2? if neither are intended or true in lore, then we dont actually have an issue at all.
Vamp is funny nanomachine man, at the very least it can be handwaved based on how nano's can work. Fact of the matter is, it's inconsistent, but it's consistently inconsistent so like, it is what it is.