I understand your point.
The solution is simply what kind of games you are going to play.
In an historical scenario you know in advance what situation you will simulate, so there is no problem. Same in a friendly game, you just have to ask your opponent if he will use the same army of yours and you will have the answer.
In a tournament you can ask the umpires, but I can tell you that is impossible to meet 4 different players using the same army you choosed. You should simply organize the ally corps with baggage inside it and not in the baggage army corps.
[it] This would be the only option in a 1-list competition (which is all that is played in NZ currently). Multiple lists offer an opportunity, inefficient though it would be, to cope with the Civil War effect on the Army Bg in your OOB.
I take your point regarding the practical aspects of army selection. I'm not certain that all competition convenors would commit to advising all competitors of the others' army selections as a separate exercise to having their OOBs checked. This would be inviting selections conditional on those of the others and a good deal of recursion would ensue.
For irregulars, at least, the baggage benefit to command ME is minor. What is quite handy in incorporating baggage into a army baggage command, besides the dual counting, is the permissability of "hiding" it as a unitary clump behind terrain or troops that deter baggage raiders. Command baggage, subject to the intermingling at deployment rules, can be forced into an exposed position dependent on the role selected for their command. I frequently dispense with irreg allied baggage to avoid the attendant deployment constraints for the fighting troops in that command.
Cheers,
Ivan.
