There are several reasons why Y'Shtola and Thancred would have been affected differently. Y'Shtola was the one who cast the spell, she is a mage and she's a Miqote, while Thancred either passively received the spell or was swept along by it, is not a mage and is a Hyur.
Also Thancred came out of the lifestream by himself, while Y'Shtola needed to be pulled out.
We can't really rule out that her blindness might stem from either the casting, or from being pulled out by the White Mages. Come to think of it, the second time she used that spell in Shadowbringers, she came back without further damage. This might be because she had already lost her eyes, so there was nothing left to damage, or maybe Emet was so much better than Kan E Senna and her compatriots, that he managed to get her out without damage, where the Seed Seer was less successful.

There's of course always the possibility of randomness, or maybe there being different zones within the lifestream, with their respective different effects on the living.
Or the damage the pair suffered might not even have been from the lifestream itself, but from some vengeful entities within it, who attacked them. In the Aitiascope we saw that it's entirely possible for evil beings to stay coherent for some time and attack the living, should they come in range.