I hope to god they didn't put WALMART brand oil in your car! Hope it was pennzoil, castrol or other.
If you changed your oil frequently enough, then I don't think the filtering issue would have changed anything. It still would have worked and done its job, its just a stupid filter anyways, that's all it does.
The only thing is that your overall oil pressure might have changed if in fact the GT & GTS do take different filters. So you may have had problems engaging LIFT properly.
They most likely used a FRAM Filter, for the 1ZZ-FE FRAM calls for PH4967 filter, and for the 2ZZ-GE is PH4386. So its two different filters, but I haven't picked up both to see what's the difference yet, as I'm still getting all my oil changes done by Toyota.
But in terms of engine damage, wear n tear. I don't think they'll be any at all, unless they used the WALMART Oil.