We study fermion-parity-changing quantum phase transitions (QPTs) in platform Josephson junctions. These QPTs, associated with zero-energy bound states, are rather widely observed experimentally. They emerge from numerical calculations frequently without detailed microscopic insight. Importantly, they may incorrectly lend support to claims for the observations of Majorana zero modes. In this paper, we present a fully consistent solution of the Bogoliubov-de Gennes equations for a multicomponent Josephson junction. This provides insights into the origin of the QPTs. It also makes it possible to assess the standard self-energy approximations, which are widely used to understand proximity coupling in topological systems. The junctions we consider are complex and chosen to mirror experiments. Our full proximity calculations associate the mechanism behind the QPT as deriving from a spatially extended, proximity-induced magnetic "defect." This defect arises because of the insulating region, which effects a local reorganization of the bulk magnetization in the proximitized superconductor. Our results suggest more generally that QPTs in Josephson junctions generally do not require the existence of spin-orbit coupling and should not be confused with, nor are they indicators of, Majorana physics.