I've also found this to be a bit bothersome.. I can't say I had been able to control record/output volumes separately in the previous version, since I started on Pro 2 since I got the DDJ, but it does seem a bit odd that unless your speakers have independent volume control, you are stuck recording at whatever output you are running.
However, there does seem to be a solution... Go the the recording tab (hidden under effect unit 2) and and you can control the gain of your recordings. So you can boost up that gain, so then you can record a mix at a normal level without blasting your speakers. What I'm not sure of is whether this will affect quality...
But I think what the main issue, is that the volume knob on the DDJ-T1 is a midi knob that controls the master output in Traktor, and not a hardware knob that controls the level of output from the controller's sound card.