I think your reasoning is correct. Bit of a shame for users like yourself who need the bars on for extended periods. Is there still a layer that will stop corrosion? If so, and if you are intending having the bars fitted more often than not, the pragmatic solution would be to do nothing until you sell the car. You can then make a judgement as to whether there is enough value left in the car to make a cosmetic repair worthwhile.
Well I only ever carried a single 20kg load for less than 5 miles (garden patio table). Was anticipating getting the canoes out again but it never happened so the bars remained on and unload for a year. Thule did point me at their safety instructions which says the bars should be removed when not in use but in reality for people who canoe, ride bikes, outdoor, etc. roof bars tend to be a permanent fitting and I've never had issues like this before even after years of permanent fitment.
I would think that a long journey with a heavy load then the same would possibly happen depending on terrain, winds, etc.
Thankfully there is some paint/protection below the thin colour top coat so for the moment corrosion is hopefully not an issue. However for how long this will last after the bars have been used several more times I don't know.
If Thule/Fiat can't come up with a solution then probably the next best think I can do is to get the bars thick Chrome Plated. The only issue with this is that the end sections are clip/snap on plastic and whilst plastic can be sort of chromed I doubt there will be a continuity of look and finish along the whole length of the rails.
Interesting little problem.
Of course another solution would be to remove the roof rails completely and get the roof channel inserts. To my knowledge these inserts have to be painted to match your vehicles colour/finish and despite the cost any mismatch in the after production painting will stand out like a sore thumb unless one chooses to go completely different. My 500X is Metallic Bronze so black or silver would be required.
Why Fiat have fitted roof rails that are just cosmetic and not up to their intended purpose I have no idea.
I'm just hoping other 500X owners with roof rails who also use roof racks/bars will have the same issue so we can get something constructive and long term done. Even if Fiat agree to replace my roof rails (£250 ish) then the next time we use roof bars then the same will happen again.