Every channel and network the BBC have is different, so why should they all be formatted with the same branding exactly?
Fundamentally, they all have the core 'BBC' brand, then that is elaborated with the channel or networks individual brand reflecting its demographic, audience or tone of voice... it works!
But they're not all different - that's the point! In interest of neatness and continuity, they should all be the same/similar (like the original box logos or ITV's current branding), or be the complete opposite and have completely different logos and brands (such as Channel 4).
The BBC have three channels which have box logos (News, Two and Four) and two channels that don't have box logos (One and Three) except for when they're with the other channels. Either all have boxes, have none with boxes, or let all have two logos (one with a box, one without).
The fact that BBC One and BBC Three's make-shift box logos look bloody awful is also another reason why I think it's not great at the moment.