Programs establish consistency, which is key. As long as you're consistent in what you do, it doesn't really matter, unless you're doing stupid/useless shit. The programs in the OP happen to be good examples of what to do, and if you do them consistently, you win. I didn't follow them at all from May to mid-November. I got a lot stronger, but since then I've been focusing on the compound lifts (minus Squats), and my gains have increased dramatically. At the rate I'm going, I'll be benching 225 within a month.
The programs are GOOD consistency, and they help FOCUS your energy on the lifts that matter most (compound). There's really nothing wrong with following them.
EDIT: forgot numbers.
May - 95lb Bench. Maybe 8 times, then done.
Mid-November - 160lb Bench, 5x5
Today - 165, 175, 185, 190, 185 x5
So, 65lbs in 7.5 months. 25lbs in like 25 days? This is doing OHP, Deads, Bench, Incline, as well as Arms twice a week. That's it. All 5x5.
A wise man once said, "I know I thought I knew what I was doing but when I got into a strict program -and was dedicated to it, not missing a workout- my progress skyrocketed." True for me too.