Axel would always iniate the kisses and if Saïx was in the right mood he would allow it and if he was in an even righter mood he would kiss back and he would take control. He would kiss Axel passionately with a hint of aggression and Axel would let him, would hand over control, would enjoy it, melt into it.
But when Xemnas kisses him it's different. Xemnas doesn't care what mood Saïx is in. And even though Saïx knows it's no use he cannot help the instinct to try and take control. There's no passion, just aggression as Saïx kisses him back (because trying to get away from the situation alltogether is not an option and Saïx knows that all too well), snarling and biting into his bottom lip. He doesn't stop until he can taste blood on his tongue and that's when Xemnas pulls back and looks at him. Smirking with arrogance shining from his amber eyes and god, if Saïx could hate he would. He would rip this man apart. This man who took everything from him; his home, his family, his heart, the very life he could've lead. But Xemnas is too powerful—he could end Saïx's existence without even trying.
It's a fight, a struggle for dominance and power that Saïx knows he'll never win. Yet it doesn't stop him from trying. Even if he knows that Xemnas doesn't mind, that Xemnas likes it when he fights back. It makes Saïx sick, but still he can't help himself. He was never the type to just bend over and take it like a trained dog. Therein lies the irony of the fact that some of the less observant members of the Organization refer to him as Xemnas' lapdog when they think he's not listening.
Being with Axel is about trying to fill the empty void the loss of their hearts left within them, it's about reliving memories of their youth, it's about trying to hold onto some of that love Isa and Lea had shared. Being with Xemnas is nothing Saïx has a say about. It's about the older man's desire to put him in his place. It's about power and control and nothing else.
When Xemnas' fingers curl around his throat it's a reminder, it's punishment, it's the twisted game they play. Because Xemnas knows—knows of the treachery going on behind his back, knows that Saïx and Axel are planning something, knows that they aren't loyal to him, not one bit. Axel would be easier to break—he's the 'emotional' one, the fiery and bright one who wears his non-existant heart on his sleeve. Break him and Saïx would rebel. Break Axel and Saïx might pose a threat.
That is why he goes after Saïx. Saïx is stoic and composed and keeps to himself. He doesn't speak of what Xemnas does to him, he doesn't show it outwardly. At least not so that others notice, even if Xemnas does. He watches as Saïx grows colder and more distant and it's exactly what he wants. He watches Axel and Saïx's friendship crumble, their threacheous union break apart. Axel doesn't do well in the cold and neither of them can communicate well enough with each other to mend their broken relationship.
Xemnas has truly mastered the art of killing two birds with one stone.