I didn't mind the Pertwee/McGann logo as it became the de facto 'classic series' logo. Besides, it was at least appropriate on some of the titles.
The Whittaker logo doesn't appear onscreen for any of the boxsets. I wonder if the sets will even reach that far.
The steelbooks are a mess of Pertwee logo on some Tennant releases, Whittaker on classic releases, Capaldi and, admittedly, Whittaker and the 60th anniversary logo on classic and 60th anniversary. Absolute mix-and-match.