Certain simulators do exhibit that problem; the student may never climb above 5,000 during the entire exercise, with multiple approaches, but the FMC needs to be re-cruised in order to generate a top of descent for the subsequent approach. It sounds like the case with this simulator, something not found in the airplane, but which is occurring in the sim, with little explanation as to why it's being one. Accordingly, one could search the procedure in the FCOM or FCTM, and not find a reasonable explnation. Having to re-cruise the FMC lends to confusion in that case, especially if it's simply explained away as a "simism." The original poster described the sim instructors leaning over his shoulder and setting it in the box, perhaps to facilitate the procedure so the student won't get in the habit of learning a behavior that is only required in that simulator.
Regardless, if protecting the FAF, that's something that's done on the MCP. Other than a sim-only process of re-cruising the box to establish a TOD, then the only altitude inputs to the box might be making an altitude a hard altitude, as opposed to an above or below altitude. The instructor should explain, if there's confusion, and that's best handled both by doing classroom work, and perhaps stopping the sim to clarify, before continuing on a procedure. That shouldn't be coming up at a checkride, though; any confusion on the procedure should have surfaced and been handled well before arriving at a checkride. Definitely before the re-test. As noted before, however, despite any desire to "overachieve," don't add to the procedure or improvise. In the sim, it might result in a busted checkride. In the field, it might result in a busted airplane.