No specific experience of ATRs but I know on many aircraft types painting the rudder is a pain. When you see new aircraft just out of manufacture, the rudder is painted even if the rest of the aircraft isn't. Perhaps being at the extreme rear of an aircraft might affect weight and balance or trim in some way. Presumably you have to remove it to paint it which affects handling so requiring an air test - an expense they would rather avoid.
Hopefully an engineer or someone who understands these things can explain as I would be interested to know myself.