I think the choice (and the results) will really depend on how comfortable you are with the tools.
A long time ago I used a silver paint pen to fill in a design on a fairing. It was much easier for me to color inside the lines (so to speak) with the pen than it was with a brush, because the brush bristles were flexible and didn't always behave the way I expected or wanted.
I have also taken small brushes and cut the bristles down to make them less flexible, which seems like a decent compromise. On some I cut the bristles on an angle and the result looked like a sash brush - that was handy. If you have some disposable brushes, you can cut them into different shapes depending on the size and shape of the nicks you want to fix.
That particular paint pen (don't remember the brand) lasted a long time: it was usable 15 years after purchase, which was a little surprising.
1979 KZ400 Gifted to a couple of nephews
1967 Yamaha YCS1 Bonanza
1981 Yamaha XT250H
1981 KZ440 LTD project bike
2013 Yamaha FZ6R
I’ve used their pens and was not successful because the paint seemed to come out without fine control but that also could be down to the fact that I’m not the best (read: sucky) painter.
I think the best would be to go to an art store and by a really nice small brush. They’re cheap and excellent.
If you go with the pen, have one of those artist brushes handy as you can dob the paint from the pen onto the brush.
For touching up the frame in black, Sharpie makes big markers that use real oil paint. They’re about $3 bucks. They also have an assortment pack of smaller pens with different colors for about $12 bucks. I bought mine at Home Depot in the paint isle.
I use them also to fix any scuffs I make on my black rims after a tire change.
The marker lasts for years as does on whatever you painted.
"Swim against the current, even a dead fish can go with the flow"-somebody (I forget Who)