There was a Terminal Countdown Demonstration Test (TCDT) performed late in the training flow for each mission in which the crew would fly out to Florida where their Orbiter was stacked on the pad.
This constituted a full-up simulation of the countdown with the firing rooms staffed. Intrusive/extra-expensive activities weren't done - no fluids were actually loaded into the External Tank, and the pilot did not actually start the Auxiliary Power Units (APU), for example- but actual crew station switches were thrown and the crew was strapped in, in the vertical, in their suits. The Orbiter was powered up and switches thrown resulted in actual system responses.
The TCDT ended with a simulated pad abort where the crew would practice unstrapping, climbing out of the Orbiter, and running over to the slidewire baskets (but not actually riding them down).
There was no "sim mode" for the Orbiter controls. When the pilot was supposed to be starting the APUs, she or he just called out the actions and didn't actually move the switches: "Simulating taking APU Controller Power to ON!", etc.