Before I begin here I know we should not think too hard on this stuff or the whole premise of the game quickly falls apart. But I'm going to anyway! It seems to me that Fallout 4 has a lot of magic in it. Certainly most things can be explained with "because science!".....but some just CAN'T. Examples:
1) Cthulhu stuff...like Dunwich Borers
2) Overseer's Guardian - science just can't make a ballistic weapon fire two rounds at once.....unless that weapon has TWO BARRELS.....or you can only fire it ONCE and you WILL take damage!
3) There is an abundance of clothing that has what I can only call "enchantments" on them:
Lucky hats - increase luck +1
A leather shoulder/arm piece that SOMEHOW gives the wearer +1 strength & +1 Endurance - hows THAT work?
answer?
MAGIC!