There is no life more full of sacrifice than that of a mage.
As much as he likes to tell her she - they, them - has broken the jinx, that she has proven that a magic circuit doesn't have to mean endless suffering and struggle, Rin knows better. Maybe he isn't just saying it - no, he definitely keeps telling her because he honestly believes it, or at least because he wants it to be true. So she doesn't disabuse him of the notion. For once. But she knows better.
It isn't that she doesn't love him, after all.
What she feels for him is solid, enduring. Looking back, she can hardly remember a time when she did not harbour even a secret, in-need-of-being-squarely-dismissed affection for him. It is a time-honoured sentiment, as integral to her person as her love for Sakura. It was a silly, counter-intuitive crush, yet it lasted. Of course it's true. She wouldn't have it any other way.
But his hair is still red. His eyes still brown. The only tan his skin knows is that of the sun, and his body is only flesh, blood, and a lost little magic circuit.
He is everything she ever wanted, but ever since the Holy Grail War, it has been only 'close enough'. He is almost perfect - no white hair, or a being forged like steel into a form it was never meant for - but the harder she craves him in any way, shape or form, the more avidly she feels all the places where, as they are now, he doesn't really fit.
She doesn't know how it happened. It wasn't always like this. It had never been like this, because despite the seductive whisperings of her feelings, she and Archer had only ever been Master and Servant. The memory of him, of their partnership, had been just another reminder of all the things she wouldn't allow herself to have. A sister, an enduring love, a cheap fling. None of that, not when the sister was a rival mage, the fling a Servant, the beloved Shirou.
Such was the life of a mage. It didn't start to haunt her - not to this degree - until Shirou's returned affections had wormed their way into her life fully and irrevocably. Until she suddenly realised that, by some miracle, she had everything she had ever wanted. That the world had turned upside down.
Rin is a mage, though, and there is no life more full of sacrifice than that of a mage. She has known that since long before she met him, let alone his other him. Just because Archer (good, loyal, suffering Archer) made it seem okay to be discontent with fate doesn't mean Shirou can cure an ache so much older than the balm of his presence.
In his own way, Archer had been a mage. Shirou would never be a mage in any way, shape or form. Rin wishes she could be above letting the difference matter, but she isn't. The denial that had shaped and then reshaped his fate is both what draws Rin in and what pushes her away, rubs salt into old wounds that no amount of denial and revolution can heal. Whatever miracle Archer worked to change the path his younger self would take, there is no undoing Rin's. A mage is not what Rin will be, it is what she is and always has been. There is no returning from what she has forged herself into, no undoing the sacrifices she has made, no forgetting.
Perhaps the true meaning of being a mage is to always want something you can't have - even if that something is to stop being a mage.
There's no reason to condemn Shirou to that old, miserable fate by saying anything, though. After all, no matter what she wants, it's not like she doesn't love him. Even as he is now.
(It still wouldn’’t make him him, anyway.)