Hi @Daniel Park
I can't speak for everyone else, but my general rule of thumb is I use GSAP to set() everything I plan to animate. If a property is not going to change, I use my stylesheet. If you're triggering animations on scroll, you wouldn't even need to set() them. You could simply use a from() tween and they'll be all ready for you to tween when you hit the scroll trigger.
As far as performance and the FPS drops you're seeing, we'd have have to know what you're animating. Are they large SVGs and pushing the browser a bit too hard? Ultimately, GSAP is animating values and a lot depends on what you have moving on the screen and how hard you're making the browser work.
I'm not sure if that helps at all, but that's my two cents worth. Others may jump in here as well.