Electronic – Differential Amplifier circuit

Here's what the output from the AMC1200 looks like: -

As you can see either output will swing from about 1.3V to about 3.9V and if you used a normal differential to single end converter, the minimum voltage out would be 2.6V to 7.8V.

I suspect you have a 5V supply and don't want to over-complicate things with adding a 10V positive supply (and possibly a small negative supply) so that you could use an instrumentation amp like the AD8221: -

But, if you do think this complication is necessary then that's fine. You don't need a gain set resistor but you do need to set an offset on pin 6 to set the "mid-point" or neutral position of your output. The AD8221 is good for over 100kHz so no problem there.

On the other hand just use one of the single-ended outputs from the isolation amp and I'm sure it will be just fine. You're only feeding a comparator so any noise can be easily filtered and using a Schmitt trigger should avoid multiple threshold triggering.

does cmrr value make sense for a differential amplifier if its inputs are separate and totally different voltages?

Yes, it makes sense. Consider two independent voltage sources as the inputs to a differential amplifier:

^{simulate this circuit – Schematic created using CircuitLab}

This is equivalent to:

^{simulate this circuit} Where we've defined the differential and common mode voltages to be:

$$V_d = V_{in1} - V_{in2}$$

$$V_{cm} = \dfrac{V_{in1} + V_{in2}}{2}$$