IF and it is a BIG IF, all the companies report taxable income with the exact same FEIN, then you can use Class Tracking to keep separate books for separate enterprises within a single entity.
However, if the companies are separate entities (unique ownership, etc) then EACH company MUST be in its own file and you just create sales receipts and invoices for inter-company operations. All consolidated financials would then have to be exported to excel and massaged. The ONLY QB software that can handle true consolidated financials of combined companies is Enterprise.
Oh, and just because each company uses different accounts in COA does not in any way mean you need additional accounts beyond what is on the tax forms filed by the entities - class tracking will segregate the income/expenses