Just exclude all these! The only number you need is the savings account balance, really
This is not well supported, imo. With Emma Pro, I think there are only manual solutions. You can split the transactions and exclude half or create a manual account and hide the real joint account. Not great solutions.
Another option is just to double your budget for those bills and create a fake account with the extra half…
A toggle to mark an account as “just half mine” probably also wouldn’t work for common scenarios either