The /api command is relatively new. Anything in that reference is specifically written to show in its own Blizzard addon. (The same as someone creating a wiki page.) Occasionally, new things are added. It will most likely never contain every single function.
"You'd be surprised how many people violate this simple principle every day of their lives and try to fit square pegs into round holes, ignoring the clear reality that Things Are As They Are." -Benjamin Hoff, The Tao of Pooh
As for that tool you linked, it's a fancy way of organizing the data available from simply running a loop on the ingame _G table. All global objects (functions, tables, strings, numbers, and booleans) of a Lua environment are in there.