Well, I whip my tanks myself, turn them upside-down to dump out the rust powder, and then rinse them with boiling water. Then I turn them upside down again and blow them out with scuba tank air and let them dry in the sun. When they are thoroughly dry I attach the valve and fill it. So far this has prevented "flash" rust from forming.
If you take your tanks to a dive shop to get them hydroed they are likely to offer whipping or tumbling for an extra charge. If you take it yourself to a hydro station they seem to just dump out the water used for the test and dry them with compressed air, probably not from a heavily-filtered source such as a scuba tank. Mild flash rush is considered to not be a problem however if you have rust "spots" I would want to inspect them to be sure they are not pits and remove any loose rust. Basically, before a hydro test the tester will inspect the cylinder and if it does not pass their visual they won't hydro test it so I'd say your tanks are probably OK. Personally I would not use the tank until inspecting it further but I have a bunch of tanks. As someone else pointed out the light you used could cause them to look more brown inside than they really are.