The ECU doesn't monitor the AFR all the time. There's a good deal of time that it doesn't. The HAC sensor is in place because when the ECU isn't reading the O2 sensor it determines proper mixture based on AFM readings and other fixed data. BUT, the oxygen content of our atmosphere isn't directly proportionate to the pressure... So the HAC is used to determine bigger shifts in atmospheric pressure so that the calculations can account for the difference in oxygen content as well.
Any after market fuel control should be re-tuned if you're going to be spending any significant time at an elevation that is greatly different from that where it was originally tuned.
Neo or MAFT? Two totally different systems; The MAFT isn't something I'd use to tune fueling, It's really just intended to adapt from the KVAFM to a MAF. If you meant a MAFT Pro or MAFT Gen II they can be set to monitor AFR much more aggressively than the stock ECU and to do so at times when the stock ECU doesn't monitor the O2 sensor (the same goes for the Neo).... BUT I still wouldn't rely on it and advise that the base tune be properly adjusted with this feature turned off. If the wideband were to fail you would be running on a crap tune.
Depending on how your system is setup in the end it may be advisable to delete the HAC sensor.
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