At the quantum mechanical level of particle interactions one does not have trajectories , one has probability loci: i.e. when measuring a particle how probable it is to be found at x,y,z, at time t. For interacting particles and particularly for bound states where in the Bohr model were orbits in the quantum mechanical solutions they are orbitals, with very specific quantum numbers . The Pauli principle applies to these orbitals and given quantum numbers for defining the state.
How can two particles that have mass be in the same place at the same time?
If you look at the hydrogen orbitals you will see that even the electrons can have a probability to be on the proton space, for S=0, without any interaction happening, because there is not enough energy. This probability for nuclei leads to beta decay by capturing the S=0 electron to turn a neutron into a proton wherewhen there is enough energy .
It is hard to think of a possibility of getting two Z in an interaction, due to the large masses involved, the quantum number constraints, and the weak coupling constant. The same for pions kaons etc which decay very fast to experiment with (make a pionic atom with two pions in the same state, for example). From what I know the concept is useful in quantum models of solid state for example.