If your (unswitched) grounded conductor is a tree (no loops), and your ungrounded conductors always are in the same pipe as their associated grounded conductor (except for switch loops), then there is never an imbalance.
If you leave the grounded conductor continuous in the switchboard, and run just one pipe (ignoring parallel sets) from the switchboard to the ATS, which has one grounded conductor and the utility side ungrounded conductors and the load side ungrounded conductors, all is well. When on utility power, there will be no current on the grounded conductor, but it will be a switch loop with no net current. When on generator power, only the load set of ungrounded conductors will carry current, and the grounded conductor will carry the unbalance on those back to the generator, so again the net current is zero.
Cheers, Wayne