1) Depends on local/state regulations. Smaller towns/counties aren't as strict. It's still a federal law to not touch/modify emissions components.
2) It can for sure! Tuning in general can!
3) I would hope not.. the dealer/FCA could technically point in that direction if something were to...
Welcome Cameron! We've got tons of info here... good and bad, but that's how we learn and make things better. Grab a chair and start reading and feel free to post and ask any questions you may have!
Welcome! I'd recommend tuning the truck to at least enjoy the extra power and perhaps add more smiles per gallon, or if you're a good driver more miles per gallon :) Engine tuning will allow you to take away some restrictive hard parts like the EGR/DPF, etc.
So, they want you to go away without a fix? Not a good look for FCA or the dealer.. the dealer at least should be helping so you can get to a resolution.