If the index signal is behind a gearing is a problem, not because the index happening slower or better to say less frequent,
but because the index will happen at different absolute angles of the spindle at the different rounds of the rotation and the motion controller syncronises to the index,
so this explains why the final position is not OK.
If the A/B is behind a gearing is not a problem, but the index must happen once per turn always at the same angle, otherwise the tapping can't work properly which I think I've mentioned a few times in a few threads on this forum.
And one more thing I've noticed was this:
7. Adjusting the encoder PPR from 208 (my 'tweak') to 200 (dataplate) and reversing the A/B pins did not result in any improvement.
If you reverse the A/B pins of the encoder direction in the software (is the same as exchanging the A with B) then the rigid tapping should not even start,
because the motion controller will know that your encoder is not counting to the proper direction and will wait for you to reverse the count direction,
so it should start working only if you reverse the encoder back with the pins or with the direction setting or if you change the spindle rotation direction.
If the rigid tapping starts with both direction settings then something is wrong with the encoder, then it does not count properly for sure.