Paint pen with brush? Got several small rust spots on roof

Hi.

I got this 2017 in August 2021. I didn't go over the roof with a fine tooth comb but I can't imagine all these spots were there at the time. I only noticed them recently. The nastiest one is about the size of a penny and is close to the middle of the roof. That's the only one I noticed a few months ago. I don't park under a tree and have never noticed sap on the roof.

I took this through a touchless car wash nine days ago. Last time I did that was in May. Other than that, I hand wash it. I can't say for sure how long these spots have been there. I only happened to noticed two days ago when I was hand washing.

They look worse in the pic than in person as the lighting really amplifies it. I had this same thing happen on my 2006 Fusion, which I had for 15 years. For the spots on the roof on that car, it never blossomed into much after I applied touch up paint. However, I did have some of this on the lip of the hood and over a few years it did chip away on the underside of the lip. Some of the spots on this car are on the lip of the roof, which has me worried. My wife or I don't recall getting hit by a bunch of pebbles so I'm not sure how all these small spots appeared.

I asked the local dealer for a paint pen but they said Mazda only provides ball point touch up sticks and not ones that have a brush on one end, which is what I've always used for my Fusion and Accord. I've never once tried the pen end.

Do you know how I can get a touch up stick that has a brush? Or would you try drespressing the pen a few times into a dish and then using a separate brush to get paint on it and apply from there?

As for the rust/bubbling, I guess just applying touch up paint over it is only temporary. On my 2009 Accord, it rusted in the back wheel wells, which was a common problem for those Accords and Civics since there's no plastic there. I sanded those lips of the wheel wells to the bare metal, applied primer, spray paint and clearcoat. I've done that twice. Also sanded the inside of those lips and applied rust reformer back there and later on gravel guard. But given that location, it's much easier to do that job and not be as noticeable. I am very afraid of sanding these spots obviously. I'm wondering if I have to resign to covering with touchup paint for now and take to the pros when it gets worse or just go to the pros now. But I'm not interested in dropping two grand.

Also, on my Fusion, I had a leak after rain or snowmelt coming from behind the glovebox onto the rubber floor mats and eventually on to the carpet. What happened was that right where the windshield meets frame in the corner, it rusted slightly. Water would enter there, travel down the A pillar and out behind the glove box. That was a simple fix with black silicone in a really narrow bead. Not even noticeable.

After I picked up this CX-9 in August of last year, I did do Krown rust proofing that December and was planning on doing it again.

Would you guys attempt a DYI? I don't need perfection. I think sanding it with a sanding block is not precise enough. Would need like a cordless Dremel/mini rotary toool so I can put some small sanding bits on the end. Then apply touchup paint and clearcoat.
 
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That's not new hail damage nor new stone chip damage.

The paint is rusting/bubbling up from the inside. If that was on a rocker panel, the i might say it's salt rusting it out from the inside but this is on your roof, hood, sides, etc. That's damage(maybe stone or hail) that was already there... And someone didn't prep it or paint it correctly.

You could try yourself but Ime, it's better to just see how much body shop would charge to repaint/touchup those spots.
Sand & primer is easy. Blending is always the hard part.
 
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