No, your hams and quads would not atrophy. In fact, the only real thing to suffer would be your squats . It might be okay for the off-season, but incomplete preparation for actual squats. Not just because it is not a comprehensive program. Their problem is that they don't ever train power-style squats.
Legal squats build big legal squats.
Leg presses have their place, but the most comprehensively compound movement should be done first. In this case, squats. Then, if you have energy left, do your assistance work and by all means work on your weakness. Choose a training weapon that applies to your weakness. Here at House of Pain we get many letters from a certain gentleman who is fascinated with the pec deck.