Yes, encoder scale is a parameter and can't be linked. This is probably for the best, because if you did change the scale with a few thousand turns completed the sudden change in position would lead to all sorts of trouble. Especially if the spindle is part of a closed position loop. (it would probably only be a momentary blip to a velocity loop)
It is probably better to simply scale the velocity output pin for closed-loop speed control.
If you want spindle-synchrnonised motion it gets more difficult. One solution might be to use two encoder counters sharing the same physical encoder. But you can probably only realistically use the motor-mounted encoder for spindle-synched moves in the 1:1 gear anyway.
