Multiple Accounts for Organizations based on donor activity

At the moment, we have several financial institutions that have 2 different accounts in our system. One particular account is used to process contirbutions and tickets given directly by the company, such as sponsorships and then their resulting complimentary tickets or any other ticket purchases. Then the other account is used to process gifts given by the company on behalf of their individual clients from IRA and other investment funds they manage. The gifts are processed in the system with the company as the owner and then the gift and resulting membership are credited back to the actual donor giving the money.

There was some confusion on this issue and a corporate gift that should have gone to the former account was placed in the latter. Someone asked why we can't just merge the accounts together and have all the corporate gifts and individual gifts given on behalf of their clients all in one account together. Personally I feel like that's not that best idea, but I can't come up with any good reasons why. But that's not to say there aren't issues I'm not thinking of or that might come up later. 

Anyone like to share which way your organization handles accounts like this and why you chose that process?