In a multivariate model like regression or logit, the model gives us coefficients (or utilities) that isolate the effect of each variable controlling for the effects of all the other variables. The imbalance you describe is just the kind of effect that the multivariate technique will control. We know that collinearity can be a problem for multivariate models, but that happens when the correlations between variables are very high, and the imbalances you describe will result in correlations low enough not to have to worry about collinearity, right? That's the sense in which I consider them slight. If we were computing the utilities directly via some transformation of counts we might be in trouble, but with the statistical model controlling for the slight imbalances we eliminate that source of trouble.
CBC/HB is NOT ignoring the imbalance at all.