The 2nd issue is related.

"Prices are calculated on a per night basis. Do you want the deposit to be one night's charge? If so, you can ignore the following options."

If the property is configured to take deposits of one night, then there is no trigger point at which full payment is demanded eg @7 days before arrival.

This further compounds the loss of money experienced by the 1st issue, as a booking cancelled at -3 days will likely result in the rooms not being sold again at such short notice & the deposit being withheld virtue of a cancellation policy, is not representative of the sum of all rooms for one night in the booking.

This is not immediately clear from any documentation available.

"Prices are calculated on a per night basis. Do you want the deposit to be one night's charge? If so, you can ignore the following options."

If "...you can ignore the following options." is really ONLY available for % deposits, then the options visible below the selection of deposit method must be hidden and not visible.