I think she was just letting him down easy. It would take too long to explain all the hows and whys of her current state as a dimensional traveler, or why she wouldn't be able to come back in spite having come to the First to begin with. She said what she needed to make a clean break, leaving Runar some hope and allowing him extra time to move on that, as a destabilizing aetherial manifestation, she didn't have at the time.

But it would also be very Y'shtola to actually work it all out just to come back and reject him again. My personal hope for her retirement has her as the de facto ruler of Sharlayan. Just because.