Just guessing here, but by introducing a CTA between the CTR and the TMA they may have had to add an additional layer of ATC as well.
I think it's just a quirk in the NL (in fact, only at Schiphol) that the stubs are called "CTRs". Everyone else would call them CTAs, and have the same ATSU controlling them as the CTR.
We regularly fly over Amsterdam at 1000'-1400', with the full permission of ATC (as Amsterdam lies in the Schiphol CTR). There is no space whatsoever (not even a park) on dry land to "land clear" but there are several canals and lakes that you can use.
The difference is that ICAO Annex 2 and NL requirement is
Except when necessary for take-off or landing, or except by permission from the appropriate authority, aircraft shall not be flown over the congested areas of cities, towns or settlements or over an open-air assembly of persons, unless at such a height as will permit, in the event of an emergency arising, a landing to be made
without undue hazard to persons or property on the surface. No aircraft shall be flown acrobatically except under conditions prescribed by the appropriate authority and as indicated by relevant information, advice and/or clearance from the appropriate air traffic services unit.
The UK requirement to be able to land
clear of the congested area, which is more restrictive.
Anyway, we're not talking about overflying London here, as there are specific rules for overflying London in a SEP anyway.
There are no special rules for overflying London in an SEP aeroplane. There are some that relate to helicopters.