There is any way no reconciliation except if you use the clearing.
But as this way of working is based on the global amount to pay, the user should not care about the state of each invoice individually.
To implement this workflow, the account_payment module should deduce from the payable and receivable fields the pending payments. And it will need a wizard to create a payment for the remaining amount to pay or to receive.
At B2CK, we already tried to implement a payment with many lines. Such design is very fragile and lead to a very complex code that I do not think we should maintain.
My conclusion is that the company needs to decide which workflow it wants to follow: line by line or global, but it can not have a mix of both.