I'm getting my front bumper cover replaced at a body shop my dealership recommended (on the dime of the genius who backed into my parked car). Before bringing it in I figured I'd wash and decon the car so they can match the colour more easily. 

While doing so I noticed a tiny rock chip on the roof, about 2-3 mm across. I also noticed it had started rusting and it had spread about 1-2mm to the right as the paint had kind of wrinkled a little. 

Now, as far as I know it needs to be sanded out, the lifting paint needs to be sanded too until it's all shiny bare metal. Maybe use some rust dissolver in there followed by rust converter/primer. Then paint and clear. At least that's what makes sense to me.

So when I took it to the body shop I asked if I could pay extra to have them do it because while I do work with paint as a hobby (scale models) I am not any kind of autobody expert. They told me they'd have to sand and repaint the whole roof. Now, I don't know if they were serious or just didn't have time to do it/didn't see it being worth the money to do so and didn't want to say so.  

So I'd appreciate the opinion of any professionals here. Should I go to a different body shop and see what they can do? 

I've added a pic zoomed in and taken on macro focus. 

My alternate plan is to sand it down, remove/neutralize and paint it myself just to be sure I kill the rust before it really spreads and if it looks like shit, get the roof wrapped black which I kinda wanted to get done anyway.

Repairing a tiny rock chip w/rust