I about this did not think. Probably in servocontroller on AtMega xxx this is not got, it is necessary to use more "powerful" specific microcontrollers.
But usually in expensive professional CNC machine two encoder use as follows: 1 encoder is installed on gross servomotor (without backlash) and signals with he enters on servocontroller, 2 encoders (linear) is installed on CNC machine and signal with he enters on CNC program (for correction of the exact displacement).