Linear encoders are all metric as far as I know. Normally available in resolutions of 0.1, 0.5, 1, 2, 5, and 10 microns, this is true for both glass and magnetic scales. 1 micron resolution = 25400 pulses / inch, or 0.000039 inch / pulse.

If you are planning on closing the loop at the drive level, I don't know how a drive would react to being fed with an encoder that it was not calibrated for. Depending on the drive, it may be possible to set the scaling.

To really take advantage of linear encoders, you would need a real motion controller between Mach3 and the drives and close the loop at the controller. Dynamotion or Galil would be good choices.

I have 1 micron magnetic linear encoders on all of my machines and have had very good luck with them.