Har Bayis is a Mountain as the name implies. Most mountains you have probably seen look like a hump and certainly not flat on top
Originally har Bayin was not flat on top, top top was flattend by King Herod (There were actually 2 second temples, the original plain one and the Herod Temple)
On top of Har Habayit is a plaza (You can google pictures of it) it doesnt look like a mountain at all
The Kosel is the reataining wall used by herod to help make the top flat like the Plaza that it is