I woudn't say it's like two different modules, but it is two separate channels of the same the module. They can differ slightly to greatly depending upon how it is wired. The stock dual channel modules from Egnater are very simliar from CHA to CHB, but if you get into the modded they can wire the channels quite differently betwen A & B. For instance my JF Voxless can be a very chimey clean on CH A and quite aggresive on CH B. I would say the dual channels are more useful in a live setup over a studio setup. Keep in mind these two channels share an EQ, modded or not, and some people find that to be the deal killer. I've had several amps that share EQs in the past and don't find it to be unacceptable. It isn't ideal, but it is certainly workable. YMMV.
EDIT: The channels are switchable in an Egnater amp/preamp: M4, MOD100, MOD50.