A three phase power source applied to a full wave rectifier generates DC with something on the order of 5% or less distortion (residual AC in the output). I don't recall the exact number but it is in this range . When you create imbalance in the phases, then the residual AC increases. On a GS the AC is in the audible range and varies with RPM.
On my GS750 which idled quietly it was actually audible when the leg was switched in and out and would lower the idle slightly. It was obviously as well looking at the AC using a scope. Other than creating more ground bounce (i.e. noise) it is not really an issue as pertains to "imbalance".
You can get an idea about what this means from looking a this chart. It shows the residual AC from ideal rectification. If the three legs are different it just gets more AC at the output. You can use higher number of phases and teh conversion gets better but as you can see more complicated. 3 Phase is popular because of this low distortion with only 3 phases at 120 degrees relative phase difference.
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