For instance, if the father wasn't a custodial on the account he can't deposit money in the event he needs it.
When did that start? I've deposited money many times into other people's accounts without problems; you don't even have to show ID -- just fill out a deposit slip with their account number and hand over cash.
In person? Not sure about that, but I know that recently I tried to set up payments between BofA and WellsFargo and I wasn't able to do automatic or online transfers of amounts over $1000.
When I was younger I had a joint custodial account with my father, for a similar purpose, though it wasn't my primary checking account. It's much, much easier to move money between two accounts you control.