I think the key point is that the Pauli exclusion principle is only concerned with electrons that are part of the same coherent wavefunction. In other words, if you have two H-atoms, A & B, separated by a distance of 1 meter, they can effectively be considered to have separate and independent wavefunctions. So it is no problem if the 1s electron in atom A has precisely the same quantum numbers as the 1s electron in atom B. However, if we move the two atoms close enough together so they start to interact, all of that changes. The interaction splits the energy levels that were degenerate at large distance, and you have to talk about the overall wavefunction of the system, and now the Pauli exclusion principle applies to the molecular states.
If you want to get into the more philosophical aspects of this, I think the answers probably lie in decoherence. The reason that two widely separated H-atoms can be considered as independent systems is that, even if they start out as part of the same system, as the separation between them increases, the amount of energy it takes to perturb the system and induce decoherence decreases until it is negligibly small. At that point, even vacuum fluctuations can break the coherence of the two-atom state. One that happens, the two atoms are independent systems and the PEP is no longer relevant.