Alright got into contact with them and:
(1) They've advised me to also register under "Self-Employed Individuals, Business and Practitioners"... yes I've explicitly and in no uncertain terms stated that I'm PAYE ..
(2) They've acknowledged that you can't file and pay online via the "Employees (PAYE)" section.
(3) They've also stated "For years previous to being registered for Income Tax you will still be able to use the 'Employee (PAYE)' site to make your claims."
So I'm interpreting this as people who are PAYE and who do Form 11, DWT etc... are exceptions to the normal criteria of "Self-Employed Individuals, Business and Practitioners"....