The Z axis data is the phase component of your measurement and by default Auto Delay is enabled in analysis and it does remove the time-of-flight - but whether its precision depends on a couple of key factors:
1. (And most critically) Is the source speaker used for the measurement calibrated and are you applying both output EQ and correction?
2. The speaker's calibration ultimately depends on the measurement microphone used and even measurement microphones do not have a flat phase response over their entire operating passband. Are you measuring your phase over a range that the reference microphone has a flat phase response or have you loaded your reference microphone's phase correction?
The easiest way to measure a DUT microphone's phase response is to use the substitution method. That is, first measure a reference measurement microphone, then substitute your DUT microphone in place and use post-processing - curve division to find the magnitude and phase response of your DUT microphone.
Examples of both of these microphone measurement techniques can be found in the SoundCheck x.xx > Sequences > Microphones folder.