Manaz
1000 Posts Club!
1) Should I still try to re-bed the brakes?
You can try re-bedding the brakes. You may have a fair bit of pad deposit to remove. This won't fix the issue long-term, as the problem appears to be with the pad material/manufacturing.
2) Whether or not I could get the brake job done through Kia, should I look into getting aftermarket rotors and pads so I can avoid this issue? I understand that aftermarket parts aren't perfect either, but it's something that should be explored anyway. And I don't have to worry about voiding warranty or whatever because the dealership already said it won't be covered under warranty.
I'd certainly be pushing for Kia to cover it. Tell them that you've been having the issue for a while, and that you're aware of a number of other people who have had the same issue and had it fixed under warranty. Ask them what they're changing to fix it.
To be clear here though - if you have the same issue that many seem to be having, there's nothing wrong with the OEM rotors, they're not the problem. Rotors simply don't warp. The issue is that the US-market pads appear to dump deposits onto the rotors, which causes the issue.
If they refuse to fix it under warranty, you can absolutely move to aftermarket parts - they're a wear and tear item, so Kia shouldn't withhold warranty because you replaced them with appropriate aftermarket parts.