I have cropped a tif file using latest elevation lib, e.g.:

eio clip -o dem.tif --bounds 35.079732 30.901217 35.845468 31.870474

Then inspected the CRS of the file using rasterio, which returned "EPSG:4326", plus some point inside the area (lat,lng), which returned 69:

import rasterio
with rasterio.open('my.tif') as dataset:
    print(f'CRS: {dataset.crs}') # output EPSG:4326
    row, col = dataset.index(lng, lat)
    elevation = dataset.read(1, window=((row, row+1), (col, col+1)))
    print(elevation[0, 0]) # output 69

I'm new to this field, but looking up EPSG:4326 says it is "WGS 84, latitude/longitude coordinate system based on the Earth's center of mass, used by the Global Positioning System among others."

Does this mean the generated tif file contains heights above the WGS84 ellipsoid? I'm confused because we have an independent and highly-accurate measuring system that explicitly reports 69m above MSL and NOT above the ellipsoid. And that system also tells us they are ~20m apart at that point, so they can't both be right..

What am I missing here?