Here are my thoughts on the subject,
Boosted boards use an encoder that doesn’t measure the motor (thus saving space and making the motors cheaper), instead they measure the position of the belt as it turns the drive wheel. I don’t know if this encoder is required for operation.
Boosted board motors (see above for encoders) might have some degree of timing sensitivity with the encoders. You should try to match or exceed the boosted motors (not hard given that they’re not actually very good motors as far as size and power go). If you can swap it out with your own thats a win!
Boosted boards are build with 12s1p batteries (do note that they use 26650 cells that cont. discharge at a max of 70Amps and peak around 130Amps). I would not suggest using a battery pack that cannot match the stock discharge rate of 70Amps out of a fear of battery damage and meltdown. By increasing your parallel packs you can match discharge rates. For example, 12s3p 18650 cells with cont. discharges of 25Amps would provide you with a combined discharge rate of 75Amps.