It makes no sense for anybody non-Klingon to do such a drastic refit on the bridge and not replace the Klingon knobs with English or Vulcan ones in the process! No, the ST4 consoles and pulpits and whatnot had to preexist somehow.
So, the obvious explanation is that Kruge had two bridges. One for flying the ship, as seen in ST4, and another for doing some other stuff; several possibilities exist. Remember that Kruge seemed to be some sort of a spymaster operating deep within UFP space if necessary. He could have set up a special command center for his spy ops. Or the ST3 "bridge" could have been the main gunnery station. Or, since an important feature of the BoP (indeed, apparently a driving factor in its strange, prominently winged design) is its ability to land on planets, perhaps BoPs have a special command center for coordinating surface combat operations?
It's not all that unusual for small vessels to have multiple command locations. Contrary to conventional wisdom, the creation of a do-it-all nerve center is something more easily done when one has enough room, say, the room afforded by a medium-sized vessel. Thus, a small torpedo boat may need to divide its command functions so that the engines are commanded from the engine room, a separate gunnery control room exists for aiming the secondary weapons, another for the primary torpedoes, a belowdecks helm station handles the steering, and a separate bridge topside caters for sighting. A larger frigate may coordinate most of those things from a belowdecks room, leaving only the sighting function to the separate topside structure.
Timo Saloniemi