A variable focal length (VFL) lens system is utilized to determine surface Z-height measurements of imaged surfaces. A controller of the system is configured to control a VFL lens (e.g., a tunable acoustic gradient index of refraction lens) to periodically modulate its optical power and thereby periodically modulate a focus position at a first operating frequency, wherein the periodically modulated VFL lens optical power defines a first periodic modulation phase. A phase timing signal is synchronized with a periodic signal in the controller that has the first operating frequency and that has a second periodic modulation phase that has a phase offset relative to the first periodic modulation phase. A phase offset compensating portion is configured to perform a phase offset compensating process that provides Z-height measurements, wherein at least one of Z-height errors or Z-height variations that are related to a phase offset contribution are at least partially eliminated.