In difference from incompressible fluid flows, microscale gas flows commonly couple the dynamic and thermodynamic fluid states, through the combination of bulk- flow evolution and external boundary conditions. While the thermal boundary conditions have a significant effect on the generated flows, traditional studies on rarefied gas systems have been limited to gas-surface interactions where the surfaces temperatures are prescribed. Such an assumption, however, may be of little practical value at unsteady conditions, where the surface temperature can only be imposed indirectly through direct prescription of the boundary heat-flux. In this work, we demonstrate the impact of replacing an isothermal surface condition with a heat-flux condition in a variety of unsteady micro-flow setups. These include problems in acoustic wave propagation, active flow control, and shear-driven flows. Extensions to other setups, including hydrodynamic stability problems, are also reviewed.