Paragraphs 3.3.1 and 3.3.4 do seem to be somewhat contradictory:
3.3.1 At the discretion of the examiner a manoeuvre or procedure of the test or check may be repeated once by the applicant.
3.3.4 Initial skill tests for the PPL, CPL and IR are subject to a restricted list of permissible repeat manoeuvres and only the following items may be repeated at the discretion of the Examiner: (Includes Section 5, Item c).
Perhaps it would have been better to specify in 3.3.1 that restrictions of 3.3.4 apply?
The weakest points of most Skill Tests I've seen are:
1. PFLs. Often rushed and flown with little attempt to fly a sensible pattern. Glide speed excessively high, flap often taken far too early. Applicants who have been taught the 'RAF' method often perform better than those who haven't.
2. Circuits. By the time the applicant arrives back in the circuit, he/she is often quite weary, so the circuits are often rather ragged. Landings are usually safe, if sometimes less than refined!
3. Practice Diversion. Sometimes I conclude the practice diversion with a join, circuit and go-around at another aerodrome. Applicants can usually find the aerodrome successfully, but their subsequent join and circuit are often rather weak.
Some examiners report weakness in navigation. However, I've found that applicants who have been taught Standard Closing Angle correctly have no real problem. Similarly, those who have been taught a diligent technique for practice diversions have little problem compared with those who are too keen to rush into the diversion.
Good luck!