One important aspect of accurately modeling diffusiophoretic transport in a crowded intracellular environment is the correct treatment of the boundary conditions at each surface. In particular, we must capture how substrate flux interacts with objects that either block diffusion or actively consume substrate. We achieve this by imposing a Neumann boundary condition for passive "blockers" with zero flux, and an assigned consumption flux for "active" blockers. Meanwhile, the test BMC experiences phoretic slip determined by the local substrate gradient. Handling these interactions consistently requires that each domain boundary-vesicle, blocker, and BMC-be explicitly included in the finite element mesh. By refining the mesh around these boundaries, we ensure that the sharp gradients forming near active or blocking surfaces are resolved, which is crucial for matching the analytical predictions in simpler geometries. Moreover, because we treat each boundary distinctly, the same numerical approach can extend to scenarios where multiple blockers have varying radii or consumption rates, making the model highly flexible for future studies.