I'm quite aware of the pitfalls of encoders. The way I have it, I get 3000 clicks of the encoder per wheel rotation, the max wheel speed is over 2 revolutions a second, and I have an encoder on both Left and right side power tracks.
I have a dedicated Arduino that i built into a motor controller, all it does is count ticks and PWM an H-bridge, and with the way i wrote my code, it has time to run a 37 Hz PD controller around wheel speed, and measure battery voltage and current. Also, of course talk to the main MCU at 10 Hz. And it's only an 8 Mhz arduino.
So, yeah, I want my encoders to be on my motors to keep them protected inside the chassis, and they work fine doing so. And, with a lower gear ratio, it will actually be less work to count fewer encoder ticks for the same speed. Not to sound too defensive, but suggesting I get rid of my motor side encoders is not an option.
I'll look at these and see if I can remove there gear boxes and replace mine with them, as that seems to be the only option right now.