If the fueling is the same (it may not be) the two cylinders will run at slightly different temperatures. In the past, engines have been made to have different compression ratios to try and even this out.
Stems from the fact if number 1 cylinder fires at 0 degrees, number 2 will fire at 360 + the angle of the V which means from that datum, the next firing of number 1 is 360 - the angle of the V. So if you like, number 1 is early, number 2 is late.
I'd not expect a big difference on the exhaust note, but the fact of some difference does not perturb me.
