All frequencies are derived from an "about 30KHz"* base frequencies, which is divided the number of times given by the value in the 5-bit frequency register. (30KHz, 15KHz, ..., 30KHz/32) This "scale" is defined by hardware in the TIA Television Interface Chip (an Atari custom chip designed by Jay Miner), which is where all the "magic" of the VCS happens.

Edit: *) There is a 31,440 Hz clock frequency used to produce NTSC signals and 31,200 Hz for PAL consoles. This is probably also what is described as "about 30 KHz" in the manual.