making an account inactive is just to get it off some lists

So if the account has transactions in the date range of the report, it will show on the P&L regardless of whether it is set to inactive or not.  There used to be a setting for do not show zero balance accounts, that might help if the account fits the criteria.  Other wise all you could do is create "unused dummy" accounts in one company so the listing will line up

Yes ALL accounts mean just that, all of them inactive and active.