I think one key thing that is being overlooked here is in part because of the concept that Team A playing short is to their disadvantage. Under previous rules that was without question the case since the "missing" players had to be "skill" players due to the alignment rules. You always knew who the ineligibles were without any 2nd thoughts. This change, depending on which side of the fence you are on here, changes that.
The concept that led to this rule change, the idea that we should not be penalizing Team A for an alignment which is arguably to their "disadvantage" is a noble one, but it has introduced a new problem that we should not have to sort out.