Brave wouldn't know if the cookies were collected during a Chrome first-run, or explicit user navigation. They could also be picked up by direct chains during normal browsing.

To my knowledge, this type of knowledge would require updates to the underlying cookie specification itself, where additional meta information records the type of action responsible for setting the cookie (automatic vs user-navigation). But then, I would assume, everybody storing cookies would do so as 'user-navigation' to avoid getting cleaned out.