Agreed - that would definitely have been the better approach. But in the absence of that, then the next best thing is to at least be consistent with whichever logo is chosen.
In the days of the original VHS releases, they chose to go with the classic 'diamond' logo introduced for Jon Pertwee's final season and used throughout most of Tom Baker's era. They kept that on all of the releases regardless of which era the stories were from until, unfortunately, they decided to go the the 1996 TV Movie logo for all subsequent releases after that was aired.