Red Sun - I think it's a lot more upbeat because Sundowner is a lot more open and honest, as well as at peace with himself, than other bosses are. That's why it's a lot more "happy" than other soundtracks. Sundowner contradicts past game villains, and Metal Gear Villains, by being bluntly open in comparison to extremist liars.

The Only Thing I Know For Real - It has way less synths than other boss themes because Sam is not very cybernetically enhanced compared to other bosses - only his right arm is cybernetic, other than that, he's purely human, just in a powerful exosuit that makes him comparable to cyborgs. In extreme contrast, we have...

It Has To Be This Way - It's almost entirely made up of synths because Armstrong has so much nanomachines that he's even stronger than a cyborg - that, and nanos are commonly used in cyborgs, as indicated by Sam's dialogue in Mile High before Monsoon's fight. Because of this, Armstrong may as well be a cyborg because of his nanomachinery and sheer strength.