Will an aftermarket paint job last as long as an original factory finish?

My 2007 Honda Pilot that I purchased brand new and have owned for less than 2 years is developing rust all over the vehicle. Honda has tried to clay bar the rust out but it returned the very next day. Now Honda wants to sand and repaint the entire vehicle. I am not comfortable with this and since I paid for a factory finish- that's what I want on my brand new car. How does an aftermarket finish compete with a factory finish? Will the cars value diminish considering it had been entirely repainted??Will an aftermarket paint job last as long as an original factory finish?
A factory paint job is usually somewhat better unless the shop does exceptional work....tape lines can be seen unless moldings and trim are removed and/or replaced....factory robots spray a more precise amount but a competent painter will do a good job abd not be noticeable to the average person. I usually recommend that any measures that can be done are the best to retain the factory finish.


What kind of ';rust'; problem are you having? Rail dust? brake dust? Those can be tricky to get out entirely...oxalic acid (wood bleach)works in some cases better than clay bar method. Is the rust reoccurring around wheel wells...side panels? Do you live or work next to rail yards or tracks?Will an aftermarket paint job last as long as an original factory finish?
I'm a professional painter.Reading this surprises me because it doesn't seem possible that the factory paint could be doing this.I would guess that some sort of iron deposits are getting on the finish and quickly rusting.However,it's only a guess.Whatever the case may be,I wouldn't jump in to repainting it until I was certain of the cause.The new paint may suffer the same fate as the old one.As far as your question about the quality of a repaint,it's as good as the people who do it.A Honda dealer should be top notch in that respect and give you a lasting and undetectable paint job.
some times they do depending if you have who ever paint the car and it all depends on how they mix the paint and additives to it and the right amount of all the add ons that it takes along with the temp.and most of all how yo take care of the finish your self and the right wax that you use to care for your car and its shine