when there is a considerable amount of transactions happening in a large business, it is better to use the Reference field to enter the transaction reference number provided by your bank. this is because your customer/supplier has only this information along with the amount provided by their bank. if an issue arises and you need to check and verify an old transaction it would be easier then. you may also cross-reference with the amount but that would not be helpful in most cases when you are receiving or paying for multiple invoices in a single bank transaction.
i had already suggested on the forum to have timestamps. but that got lost in the crowd just like many other suggestions.
a response from @lubos back in 2014 indicates he had plans for the same but am not sure if its still being considered.