There is a difference though: A hydrogen atom is slightly lighter than it's constituents. That's why it is stable. However, the nucleons are much, much heavier

There is a difference though: A hydrogen atom is slightly lighter than it's constituents. That's why it is stable. However, the nucleons are much, much heavier than the sum of the quark masses. Which is strange, because it means that naively, the unbound state should be preferred. But it isn't, instead, you have confinement!