Your concern is valid. especially in high humidity area's of the country.
The bigger issue may be the shop. this is not a new problem and over the years there have been many threads regarding "slow body shops". A couple facts: for the most part body shops run on a tight, if not negative, margin/cash flow most of the time. Therefore they will work for the cash. Be it private or insurance work. Also, if you don't show up on a regular basis (two to three times a week) you will be pushed out for the guy that does show up. Most ask for some kind of money down. It's not wrong however, if you paid a percentage of the the total, it's probably paid too far forward. Odds are your money did not go to your project but to the guy ahead of you. Again nothing wrong with that as long as there is progress on yours and they make it right in the end.
Having said that, here is my experience; When the shop started my '64 B Body i had an agreement to pay Weekly, a reasonable amount for the work. $500. This would be posted against my running total as shown on my continuing invoice. I would pay for the supplies as we went. Again shown on the invoice and checked against what was a reasonable usage. I paid for ALL finishing products (primer, sealer, reducer, activator, color, clear, etc.) as invoiced as a pass through of cost. Of course I realized that there was a mark-up but it wasn't out of line. There was total budget number discussed and if we ran into something that would push the number higher, we discussed it. The last part of this is; And the most important) I dropped in nearly every week day. Not to be a pest or to complain, just to check in. either on my way to work or on my way home. I would occasionally bring a cup of coffee for the guys and even bought Pizza once. I was originally told the project would take 4-5 months. It took 8-1/2. The deeper we went, the more we found. But in the end it was right and I was happy.
maybe a bit long winded, but i'd hate to see anybody get their car neglected.
So.... TF360, you ask if the surface rust is a problem? My answer is; No. The surface rust is the symptom of a potentially bigger problem. You may have a bad body shop. Only you can decide.
Good Luck. Keep us posted...