The Zmanim Project uses sea level by default to calculate sunrise and sunset. They rationalise this by referencing a machloket on the subject.
I don't have access to the sefer זמנים כהלכתם, otherwise I would simply look up the reasoning there. On my own I simply can't comprehend why you should disregard the time that an observer, wherever they might be, actually sees the sun coming up or going down the horizon. In Johannesburg it makes a different of up to 6½ minutes.
Can anyone read up what Rabbi Dovid Yehudah Bursztyn writes there, or otherwise explain his logic?