I haven't tested that ""feature"" yet :-) but it doesn't surprise me at all. Normally, if the COA's are different, then you consolidate on the main accounts or even the account groups. I'm guessing here, but I imagine that the theory is that nobody wants detail for multiple companies on their financial statements.
Not much help, I know, but I suppose you could create the missing accounts in the other companies and set them as inactive.