I could be wrong. I just always assumed for anything larger than a very small nick, touch up paint wouldn't cut it. That and it can easily look bad if you don't know what you're doing.

 

touchup paint Is mainly used to prevent stuff like rust and paint chipping from damages. its never going to blend perfectly and will always be visible. if that bothers the owner the only way is to get the entire part repainted which is costly. that is why u use factory touchup paint as an alternative. the larger the cover up the more noticeable itll be. that's jus life lol.

 

The OP’s description sounds like surface rust. Surface rust is easily repaired unless it’s penetrated the metal (at least 5mm).

The big problem is internal rust. That is rust that starts from the inside (example is a fender well) and penetrates to a “bubble” on the fender’s surface. I’ve dealt with this, and it’s the worst case scenario. The only fix that works is cutting out the metal and replacement (very expensive).