I worked briefly with a company that manufactured surveying equipment back in the mid 2000's and they had a similar setup (single sensor though). They could get sub-millimeter precision as well, but they had to 'chirp' the light power modulation from very long (e.g. 1km) to short (sub millimeter) in order to remove any aliasing that would occur when the distance was a multiple of the measurement baseline.

If these are 90 degrees out of phase I don't know how they eliminate that possibility without doing something similar. (e.g. imagine the modulation is at 30MHz and your measurement interval is 10m, how would you differentiate between 20.034m and 30.034m?