I find they hold up okay for a day or two at room temperature after baking without softening much, especially you add on top of the cookies right after baking.

I wouldn’t recommend bringing the dough back up to room temperature, since you’d need to chill it again to help the dough set back up, but you can add chips & pretzels to the tops of freshly baked cookies. (There’s a good example of this in our Christmas Kitchen Sink Cookies)

Do those soften after baking when stored in an airtight container as well?
Could I pre make then let it come to room temp and then mix in pretzels and potato chips?

Yes! One caveat – If you’re adding pretzels or potato chips, they’ll soften overnight, so those are best added the same day. (or on top after baking) Otherwise, yes! And, since the dough will be much more firm, you may need to let it sit at room temperature for 20-30 min before scooping the next day.