SDC for ALTCLKCTRL

There's nothing stopping you from doing it. Are you saying that the tool is reporting that the output of ALTCLKCTRL is an unconstrained clock? Like I said, if you have other clocks that don't go through the mux, you would need to create generated clocks on the output of the clock mux as references. The reason you don't need to in your case is that ALTCLKCTRL is not generating a new clock. PLLS do create new clocks based off of other clocks.