You can still get contamination in the threads, depending on how they are cut. They're bound to have small laps and burrs. Not a huge problem IF you're aware and then able to subject the tanks to a very good clean, which might be outside the abilities of those testing.Regarding penetrant indicators contaminating the defect - wouldn't that only happen if indeed the defect is a crack and not just a surface mark, in which case the the tank is garbage anyway?
In this case penetrant test is of not point since you can already see the defect, you'd want to try something else in order to establish whether crack or mechanical defect.
Often penetrant is simply used as go/ no go, with suspect items being sent for further evaluation