They have the two inputs to FREQM (ref/msr) specifically coming from GCLKIO, so hard to see how this is not correct as there is no other way to use it.
It is not correct to use it for unstable inputs. I really have no idea what was the though behind FREQM, I have never seen it used for anything useful in practice. It might be useful to automatically detect supplied clock frequency or something like this, but I don't know how you would use that in practice.
But if you want to do typical frequency or duty cycle measurement, then use a timer, just like for any other MCU.
If you lose the msr clock, I would think you simply get a 0
You will most likely get last synchronized value.
value when the measurement completes, and if you lose the ref clock then freqm remains busy/not done so would require a swrst.
SWRST would not complete without both clocks.
Having both clocks is an explicit requirement: "Each of the generic clocks (GCLK_FREQM_REF and GCLK_FREQM_MSR) must be configured and enabled."