Can you tell where in the drive train the spindle encoder is being driven from? If it is after the power belt pulleys, then it would not be affected by the input ratio.
Alternatively, providing that there is no belt slippage, and the encoder index only serves to provide a start signal for the initiation of threading, would it really matter what the speed was? The precaution for most automatic threading is that the speed command must never be changed during a multi-pass threading procedure. This leads me to think that the engagement point for rigid tapping is not absolutely fixed, but it will repeat at a given rpm and given start point.
Edit: BTW, good luck with your Polychain conversion. I found mine got to be quite noisy at high speed....so much so that I hated it. I switched to an EaglePd drive, with herringbone style pulleys and belt. Much nicer, much quieter.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)