It'll work, the only issue is that you lose z-clearance and therefore the y-axis has to be higher up. By doing this the spindle/router mechanism has to drop further below the Y-rail to reach the work and therefore you introduce a larger torsion moment from the cutter tip to the y-axis... depending on cutting forces this could be quite large compared to the relatively small torsion moment added by the weight of a stepper on top of the z screw (which in reality is quite close to the y-rail).

Another, lesser, reason to consider is that the belt drive will be more susceptible to damage/clogging by chips thrown up from the cutter... unless you add a shield which therefore increases the static weight of the gantry.