[MazdaGT_E]

Touch up pen would work temporarily but unless you removed the rust with sanding or some type of rust inhibitor the rust would still be under the touch up paint and spread like cancer,
but a good block sanding in the area, small block with 120-320-400 progressive grits then a simple, quality spray primer and then a vinyl wrap could be a cheap alternative to a full roof respray and protect against future chips and bird droppings

 

[MazdaGT_E]

Thank you.. from the 'bottom line' here.. I'm guessing if it were your car you would be sanding back to that red circle at least

Another suggestion I've had is to do just that, prime it, sand it, then just wrap the roof. If the car was white I might be keen on that!

I think that would make the car very hard to sell if the need arose...

Yessir, you are on the right track, I will always try to save myself money so doing what you mentioned before paying couldn't hurt, I would 100% sand it back to the red circle, but neatly, dont go overboard or to heavy of a grit, when in doubt, wipe the area with a wet cloth to see if you have any scratch marks from the sandpaper and if you do keep working until they're gone.
As far as the vinyl thing goes I do think it would be a hard thing to sell to a potential new buyer but its really not the biggest deal and a relatively cheap fix. if you have the skill, tools and supplies i say sand it, clean it, treat it and paint it, could be fun and a learning experience.