Hello,
I understand.
Unfortunately there’s no filter to control the deposits. Moreover I am not accepting feature requests for the plugins at this time due to the upcoming release. I only fix bugs.
The deposit is created at the IPN handler, function action_parse_request, and the fee set is the one reported by the IPN handler:
if ( 'deposit' == $_POST['ipn_type'] ) {
…
$txrow->fee = sprintf( '%01.8F', $_POST['fee'] );