I agree mostly.
Any MX-5 I buy now, will be bought on the basis that it needs the arches and sills doing. At that point I would try to pick the one that presents itself the best elsewhere.
A "rust free" car will have a higher price tag, but potentially need the same money spent on it. Better to take the guaranteed cost of repair, than the gamble and it end up costing even more.
That said there's more to consider and it all needs to be weighed up. I'm sure there's a better example out there than the one OP is referring to, unless it's basically free lol