OP if it makes you feel any better, mine started to show surface rust in the same exact spots too. I think this is because the water puddles up in those spots so it's easy to trap moisture. I noticed this very shortly after installing them too, but it was winter time and way too cold to deal with it, so I just left it alone, lol.
Anyways, fast forward to almost a year later, the rusting did not progress at all since (it remained as only surface rust), and this past fall, I just lightly sprayed it with some rustoleum rust reformer:
Followed by a couple of coats of rustoleum bedliner:
And all is good so far. Will report back after this winter and let you know if I see any more rust
Keep in mind, before installing my sliders, I painted it with the rustoleum bed liner right over the standard textured powder coating bud puts on there. I did this so it would be easier to touch up in the future since the spray on bed liner is ridiculously forgiving when it comes to touch ups.
IMO, nothing I would complain about, you have to be reasonable in your expectations; it's powder coat and powder coating has it's limitations, as several people have mentioned above. I think sharp 90 deg edges (like on the edge of that diamond plate) are just difficult to paint period.