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Ok, good to know about the recommendation on drives with local rotary encoders.

For linear forcers or brushless DC motors without local encoders, how should the independent linear encoder be wired, with respect to the motor controller and/or LinuxCNC+Mesa?

I do not recommend using the drives local rotary encoder as direct feedback to LinuxCNC.
It's possible but does not really confer any advantages. 

A system with a step/dir servo drive and an independent linear scale does have some advantages
in improving accuracy.