AFAIK there is nothing specifically about baggage having to be in a command over and above any other troops having to be in a command. DBMM says "An army is organised in to 1-4 commands..", etc - as far as I can see there is no provision for any troops to be outside that structure.
That makes sense. I agree, you are right, army baggage must be in a command.
however I stand by my analysis of the wording for army baggage - it does not say that army baggage deploys in the rectangle of a command - it says that it deploys in the command itself.
Although I can see how you could get this from the words, I don't think that the army baggage can actually be part of a general's command.. It says "it deploys in one of them" and "them" refers to commands without baggage. If the army baggage is part of a general's command, it has to deploy as part of that command. But that command is not a command without baggage (it has the army baggage). This is a contradiction.
This implies that army baggage MUST be in a train command.
"it deploys in one of them" also applies to baggage in a train command. If it means they are part of the command they deploy in, then the train command is part of a general's command as well as being a separate, general-less command. This is another contradiction. So it can't mean they are part of the command in which they deploy.
On p 22 we have "...each command with a general must depoy inside a rectangle..." The army baggage train command does not have a general so this says nothing about where to deploy it. IMO "it deploys in one of them" resolves this and means "it deploys in one of their rectangles".