You really shoudnt have to use that much subtrim. Its not going to hurt anything but it just screws up the centering of the servo. In a perfect world, after trimming a plane to perfect flight characteristics you would go back and mechanically adjust and take all the servo trims out, other than maybe a little elevator trim that is required during flight as the cg moves due to your fuel tank getting lighter/emptier.
If it were me I would make a note of where the rudder needs to be,, set the subtrim back to zero "if possible" and then adjust the clevis to get back to where you were with subtrim.
I think digital servo flutter is pretty common, due to exactly what you said, looking for their HAPPY place. Sounds like you have found a thread where you guys can work it out. there are certainly guys that have dealt with it that will tell you how to correct it.

I havent used digital servos, yet,,,, so im not sure what the process it to correct the electronic flutter.