With the motivation of determining the critical roughness size, a global stability and sensitivity analysis of a three-dimensional Falkner–Skan–Cooke (FSC) boundary layer with a cylindrical surface roughness is performed. The roughness size is chosen such that breakdown to turbulence is initiated by a global version of traditional secondary instabilities of the cross-flow (CF) vortices instead of an immediate flow tripping at the roughness. The resulting global eigenvalue spectra of the systems are found to be very sensitive to numerical parameters and domain size. This sensitivity to numerical parameters is quantified using the
$\unicode[STIX]{x1D700}$-pseudospectrum, and the dependency on the domain is analysed through an impulse response, structural sensitivity analysis and an energy budget. It is shown that while the frequencies remain relatively unchanged, the growth rates increase with domain size, which originates from the inclusion of stronger CF vortices in the baseflow. This is reflected in a change in the rate of advective energy transport by the baseflow. It is concluded that the onset of global instability in a FSC boundary layer as the roughness height is increased does not correspond to an immediate flow tripping behind the roughness, but occurs for lower roughness heights if sufficiently long domains are considered. However, the great sensitivity results in an inability to accurately pinpoint the exact parameter values for the bifurcation, and the large spatial growth of the disturbances in the long domains eventually becomes larger than can be resolved using finite-precision arithmetic.