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I'm afraid when you start analysing elevation data at such zoom levels you start to see the inherent flaws in the data; its resolution is not perfect. The elevation data is a grid of terrain elevations for most of the world, but it was derived from a space shuttle-based radar installation and it does not include mountain peaks. Mountain peaks are very separate data, typically derived from geospatial surveys, and those are the spot heights you see on our map.
SkyDemon uses both terrain elevation grid data and mountain peak data when calculating your MSA, which is the minimum safe altitude for any given leg of your journey.
The What's Here screen is designed to show you the terrain elevation value under your finger, but since fingers are large, it is inherently not a good idea to poke your finger on the screen, look at the value and decide on an MSA based on its output. That's what the MSA value in the PLOG is for.