First of all, welcome again to the forum. I'm sorry to hear about your roof issues.
Now, as for it only being repairable at the factory, Camping World just repaired/replaced the entire roof on our Springdale when a tree fell on it. That included replacing all the roof trusses, insulation, A/C ducting, some electrical work, vents, A/C, roof decking and the entire EPDM membrane. So, I'm confused by Keystone saying it's only repairable at the factory ????
It may be that after a couple of dealerships have "messed with it" that the powers to be at Keystone have said they don't want to spend any more money on it trying to fix what the dealer has not been able to repair. They probably told the customer service rep to just have you bring it to the factory and they will fix it the right way and stop the issues you're having.
Let's hope that's what is happening
As for them offering to help pay for fuel, that's a definite plus !!! I'd take the factory up on it and drag it to Indiana. Heck, it's a wonderful time of year to travel in the midwest, cool, not too much rain and fuel prices are the lowest they've been all year.
Just so you know, if you elect to just do it on your own and not take Keystone's offer to repair it, the cost to replace the roof on our 26' Springdale was in excess of $9000. It surely can't cost anywhere near that much to drag it to Indiana