It looks to me that SERA.5005(e)1 should be read in conjunction with Rule 5 (and Rule 6) of the Rules of the Air Regulations 2015 which took effect on April 30.
http://www.legislation.gov.uk/uksi/2...0150840_en.pdf
It would seem that you may not be constrained in your overflight of the congested area of a city town or settlement provided that you are en route to a landing or take off point which is outside the congested area.
But a landing or take off at a site within the congested area must comply with the requirements of Rule 5 which specifies that it must be: -
- at an aerodrome in accordance with published procedures notified by CAA, or
- if it is at landing site which is not an aerodrome in accordance with procedures notified by CAA and with the written permission of the organiser of the assembly