A typical squat should involve a neutral spine, eccentric taken at least past parallel, knees tracking but not going past the toes (which should be positioned either facing forward or slightly outwards). When viewed from the side the shins and spine should be at roughly the same angle in the lengthened (bottom) position. Hope this clears up any issues.
"Commonly overweight people do have very big calves and lower bodies. For exactly the reasons you mention: their entire life is one big progressive overload on the calves." Lyle Mcd