I understand that you want to import ADS substrates & designs into your own 3D simulator. Is this for personal use or for a competitive product?
Simulation area in FEM is always finite, so we need to define a simulation boundary, and assign boundary conditions.
Relevant for your case: Many ADS substrates are created for Momentum. Momentum uses planar MoM method with infinite substrate size. That means dielectric layers are defined only in the substrate file, and then automatically exist in the EM model, without drawing any object. But if we use that substrate for FEM, which uses finite simulation area, what is the size of these dielectric layers? That is where the simulation box size becomes relevant: it defines the simulation area and also sets the finite dimension for "infinite" dielectric layers that have no bounding area layer defined.