It applies (in very rough approximation) to groups of nucleons, which is where it was first discovered. People observed that the nucleon/nucleon scattering length was surprisingly long for what they considered natural nuclear scales (or equivalently, that the deuteron was very weakly bound). The circumstance where the Efimov effect is mathematically exact is when the scattering length is infinite. Fermions in this circumstance are described as unitary.

Sadly, the Efimov effect has nothing to do with the proton size puzzle.

Source: IAANuclearPhysicist.