Is single ended amplifier a subset of differential amplifier?
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 &ndash; Schematic created using CircuitLab

This is equivalent to:







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

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

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