The nice men at 2|Entertain. The very sound reason for it is that retailers hate bulky boxsets like the six-amray-cases-stuck-together format of the limited edition KtT one. They consistently pressure 2|Entertain to release these things in digipacks (similar to the packaging for the new series S2 and S3 sets).
However, 2|Entertain are well aware that there are many fans who really like the amray boxes or, more importantly, want all the DVDs to line up on their shelves exactly the same. It's in order to facilitate these fans that 2|E are releasing the boxsets in the format they are.
However, however, in the spirit of compromise 2|E are limiting that format of box to 15,000 units. This should be more than enough to fill orders for all the fans who are insistent about having that format. After that run has sold out (hopefully not *too* long after) the KtT will be re-released in a nifty little digipack.
That's all refering to the Ktt, of course. AFAIK the Davros box isn't a limited edition at all.