Steven,

Let me try to give you answer as per my understanding.

Paid by Employee: all the payment is done by the employee. We can reimbursement this amount and add in employee payroll. so it is directly linked to payroll.

Paid by Company: it means that company already have paid an amount to the employee and from which he is doing expense. this is not linked to payroll.

That's why you can see both the entry in the different journal, logically odoo is right. :)

Thanks.