Well QT conversion is going to use the render files as the source, and recompress them as whatever you've chosen. H264 for example. 3 hours sounds normal if you're going to the same frame size. If you were exporting something to a web size like 640x360 as a single pass encode, it's a little longer than real time. Maybe 2 hours. Matrox systems with MAX will speed up that 3 hour export to less than Real Time.
Export QT can be either. If you're just looking to make a master file, export QT, choose Current Settings, Self Contained and it will essentially be a copy of the rendered/referenced frames into a self contained file. That should maybe take 15 minutes. It does have to render the audio into a single stereo track so that takes a little time, as does the actual file copying.