This is one of the daftess rules in the game!
Due to one isolated incident we have a situation where Ps end up embedded in a formation.
This does not reflect the ancient military manuals and the ancient authors accounts of both Greek and Roman warfare where the Ps moved through the formations behind them to then act as a reserve to pursue routers. Even barbarians such as the Allemanni performed this without getting in a tangle!!!
The idea is that you use PIPs to withdraw them all the way through before they get into a serious fight, rather than relying on recoils.
NB ususally Ps will repulse from foot, which may enable them to get through all the ranks of the pikemen, depending where they start, of course.
Personally I think they should go all the way through, but then you need extra rules to deal with what happens with very long columns allowing you to teleport interpenetrating troops vast distances.