That's not any theory I've heard of. Programs generally have you doing the same exercises repeatedly. Variations are not usually intra-program substitutes, and "slight variations" as substitutes are an anti-pattern. "Many muscles" also has nothing to do with it either--most leg exercises put the largest component of stress on the glutes, which are one big muscle body. On the other hand, the back is a whole lot of different muscles but I don't think very many people do 3 back days a week.
In particular, the GP was talking about Stronglifts, which has you doing the same old back squats 3 times a week, variations strongly discouraged.
There are a lot of tried-and-true programs that include multiple squats a week.
Stronglifts is one, but there are programs from Glenn Pendlay, Bill Starr, Mark Rippetoe, etc. and they're all good for beginner to intermediate lifters - and they all feature two or three days a week of the same-old squats.
A beginning lifter should make gains in the squat even while doing it three times a week, sometimes for many months. After you hit the wall, programs will drop the number of squat days, replace a day of back squats with the front squat, or replace all-heavy days with a light-heavy-medium rotation.
It's true - you'll eventually plateau. But a 3x week squat program works for a lot of people, especially when starting out.
In particular, the GP was talking about Stronglifts, which has you doing the same old back squats 3 times a week, variations strongly discouraged.