The "inner circle" of the Companions makes up over 50% of the Companions. How it's a "secret" to the rest of the Companions is pretty astonishing.
Space compression, extended to the population. Presumably, you get to see the entire Circle, whereas the vast, vast majority of the grunts just don't show up in-game. Like most of the rest of the population of Whiterun. Basically...Skyrim is actually a lot more than ten miles across; what we see in game is a compressed representation of the actual world.
Exactly. In ESO you learn that the Companions have chartered lodges all over Skyrim, and number in the hundreds, if not more. They're an army in their own right.
Skyrim just can't depict a county 1200 miles across and populated by half a million people. Not if you want your computer to survive the ordeal. While you likely meet the majority of the Inner Circle, Jorvaskir likely houses dozens of initiates and mid-ranking Companions.