This is quite interesting what you're writting...
I understand why Tim is reluctant to change the system as the product he sells cannot create any doubts about (not)complying with the applicable rules. And whether the use of airport ICAO designators in the Route section of the ICAO flight plan is compliant or not is apparently not entirely clear.
On the other hand let me put your quote to a broader picture:
The definition you quote in your post comes from the ICAO Doc.4444 Procedures for Air Navigation Services - Air Traffic Management
which governs also the flight plans. This "core" regulation seems to be transposed to the national AIPs.
The above mentioned document states that the Route (Item 15 in the ICAO flight plan), in case of Flights outside designated ATS routes
(so I'd say in almost all VFR flights), can be filled in also by using so called Significant points (2 to 11 characters) - the coded designator (2 to 5 characters) assigned to the point
In the same document, ICAO defines the Significant point as a specified geographical location used in defining an ATS route or the flight path of an aircraft and for other navigation and ATS purposes
So the whole problem boils down to a question whether an airport defined by the four letter ICAO code is a Significant point
as defined by ICAO.
To my understanding, it is - as it is a specified geographical location.
Nevertheless, I have sent an e-mail to ICAO asking them to confirm this interpretation. Now I have to wait and see if a little General Aviation VFR pilot matters to them or not
Tim: I can confirm that none of my flight plans were returned to me because of using a four letter ICAO codes of airports in the Route section. I have been filing by paper, fax, on-line formulaire of Belgocontrol, and by SkyDemon.
Once (if) I receive an answer from ICAO I will post it here.