He's not composing notes and keys, he doesn't speak that language. He says higher, lower, darker, deeper, harder and composes his shyt that way. And he has some cat who knows just about what he means who translates it to notes and keys. Thats what a real producer does.
He's very hands on.
And All Of the lights was produced without any type of Logic, FL, or whatever the fukk. It's funny that you mention "if he couldn't sample". If he couldn't sample there would be no Kanye West. No Rza, no Illmatic, no Chronic, probably no hiphop so what are you really saying?
The only way to produce music on your own is by either being like Pharrell Williams, a master at the keyboard and combining it with drum programs and shyt like that.
Use different software to make software beats, master mad types of instruments or use samples.
Now if you wanna be a producer like the old school producers, you do like Kanye West and Dr. Dre.
It's gonna cost though.