The smart battery functions aren't really superseding anything. Those functions are independent from the battery warning settings in DJI GO.
Here's the section of the Mavic Pro manual you're referencing:
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The table at the bottom is attempting to explain what's being shown in the battery level indicator example above it (which is the indicator that appears at the top of DJI GO). DJI's use of the word "warning" is meant to describe the red and yellow sections of the battery level indicator (not the user defined warnings in DJI GO).
Check out this video for a clear explanation of what the Mavic Pro manual is attempting to explain:
Agreed - in the manual it may just be a confusing use of similar terms to describe different functions. But it doesn't explain the discrepancy between the "SMART_BATTERY.seriousLowWarning" level, the "SMART_BATTERY.seriousLowWarningLanding" flag, and the actual landing trigger percentage.