I know at my old flying school we were not allowed to teach sideslip with flap, not because the flaps would be over stressed?? but because the flaps shield the rudder and hence reduce its effectiveness. You can do it if you want too.
I'm not too sure about training to the end product rather than whats going to happen in between, unless all your flights are wholly within CTA and are also all IFR. Otherwise there are other variables at play as well.