While I have many years experience in color management and profile creation/editing, I have no direct experience with these new Apple displays.
Based on a different, long topic I was in some months back, they seem to function on the same principle as my EIZO monitor, where the calibration data (LUT) is stored in the monitor's hardware, rather than the on-board video or card.
That user had the same issue with a stand-alone Apple display and a newer model MacBook Pro as you are here. They could calibrate it with a separate colorimeter, but it would snap back to a preset profile, throwing out the calibration/profile they had just made.
Without being able to work with one of these to figure out how to get around this insistence of loading a preset profile, I'm afraid I can't be much help. Which is too bad, because there is no profile that will remain perfect forever for any monitor, no matter how much you pay for it. They all have to be recalibrated and profiled after at least a few months of use.