One shouldn't define a smooth (differentiable) manifold to be a pair $(M, F)$ where $F$ is some atlas---if we used this definition, then given any $(M, F)$ and an atlas $F'$ compatible with but distinct from $F$, $(M, F)$ and $(M, F')$ would be different smooth manifolds. One way to rectify this situation is to define a smooth manifold to be an equivalence class of pairs $(M, F)$, where $(M, F) \sim (M', F')$ iff (a) $M = M'$ and (b) $F$ and $F'$ are compatible.
On the other hand, if $F$ and $F'$ are compatible, then by definition they determine the same maximal smooth atlas, so if we simply demand that the atlas $F$ in a pair $(M, F)$ be maximal, then we can avoid involving equivalence classes as above, because by construction maximality already entails the appropriate equivalence.
Put another way, picking an atlas of a smooth manifold involves some choice, but a maximal smooth atlas is a built-in feature of a smooth manifold, and in particular involves no choice.