Extension area(E airspace) shown as shaded magenta start from 700AGL but how to measure 700AGL over the water like in this picture? Cuz there’s no land…
above surface level
This avoids the ambiguity of, ground or ocean.
When you are over the water that’s actually the easiest to measure. If you are over the water 700' AGL will read 700' on your altimeter. It’s when you are over land that it gets harder.
If you fly with something like ForeFlight you can set one of the display boxes on the bottom of the screen to show height above terrain, but otherwise you just have to use your judgement.
Looks to me like the chart is showing controlled airspace as 100/60, 100/50, 100/40 - which means the highest you can go is 4000, 5000, 6000 feet MSL and stay clear of the Class C, not AGL. So the height would be read off the airplanes altimeter. Go to www.skyvector.com, enter HAF at the top left, then select San Francisco. To the left of HAF is the explanation showing T/30, and 70/30 - in MSL.