i.e. you can't pay just the base fare and checkin online.
Correct. You have to pay £5.99 for a standard seat to be able to check-in on-line but remember there is
NO additional charge for on-line check-in.
By comparison, Jet2 charge £6 for on-line check-in which is
additional to the seat charge (unless you are travelling with no bags) and a booking fee as well.