The jrk can control speed with a single channel of encoder output. Also, it will work at input frequencies up to 2 MHz, so it can handle the 30k RPM encoder speed. However, it does not have an input for the second channel of a quadrature encoder and cannot perform position control using quadrature encoders. You might consider our RoboClaw motor controllers, instead.
By the way, 12 CPR is for both channels of the encoder and the "counts" include both rising and falling transitions. If you use a single channel of the encoder as a tachometer feedback for the jrk, it will only register 3 pulses per rotation.