Yes, I understand it's not an essential feature if using GC, payments can be captured, however even with the ~40 customers I have using WHMCS with GC, manually marking invoices as pending or paid would an incredible waste of time for something that can be automated.
I have actually just checked the developers website and it says that it does mark as pending until clears or fails ("Mark invoices as paid while Direct Debit is pending and marks them back to unpaid if payment fails or cancels." from https://www.yorkshire.hosting/portal/cart.php?gid=9) so I guess that's my question answered. Posting here for clarity as other users in the thread have also asked or had issues with this feature.