Yes, the issues are (i) that Annex 1 to the ED only requires amendments to the IR syllabus but the amendment clearly shows it as applying to the ATPL syllabus as well (ii) the timescale for introduction is confused, the CQB certainly has not got the PBN questions in it as of now.
The UK CAA appear to be suggesting a phased introduction school by school with two sorts of Radio Nav exam available, one with PBN and one without, while the introduction is in process. For my money it would be easier if they just gave us an introduction date with sufficient time to teach the material before the exams go live. There appears to be a further requirement for current ATPL or IR holders to complete PBN training (and presumably an exam) as well.
Annex 1 to ED