I had a look at both the article and the latest VFR chart updates on the CAA website. The zone extends to 2000' agl and 2NM from the positions of both Sizewell power stations, elevations 15' and 35' respectively.
Overhead at 2050' QNH is therefore legal as is 2.1NM laterally. These are close in boundaries and to the untrained an aircraft may appear closer than it is.
I cannot believe a professional pilot - must be he was getting paid for the flight - would risk all close to an obviously restricted landmark. More like the journalist did not understand where he was in three dimensions and assumed the worst.