Flow-Based Market Coupling (FBMC) is an advanced Capacity Calculation and Allocation Mechanism that accounts more appropriately for electricity grid constraints than the traditional Net Transfer Capacity (NTC) approach. While the method accounts for the impact of cross-border trades on the grid by translating commercial exchange into physical flows, the results depend on the underlying assumptions concerning the conditions in the grid at the time of market coupling. This paper focuses on the impact of different Generation Shift Keys (GSK) on the market outcome and generator dispatch. Six different GSK strategies are implemented and the effects are analyzed in a transmission grid representation of Germany, Poland and Czech Republic. The results show that the effect on the zonal level remain marginal compared to the difference between NTC and FBMC approach. However, this effect is limited to few generators, which are impacted significantly. Overall, there is a shift from flexible generation to cheaper base load generation.