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The answer from @THEGxHOxST is correct. Because the bed end stop is at the bottom (and also because the probe is not the end stop), it does not make sense to save the offset to the endstop (it would just lead to accumulated offset error over time).
Since the position_endstop is in printer.base.cfg, it can't be updated.
This is after running a print, adjusting z via the screen, and attempting to save.
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