I use a 1050 with a Sony DVD/SACD player and it seems to me that the 1050 keeps the channel levels set the same when using the Direct input. I've never had a problem with channel levels on the 1050 when using SACDs except for adjusting the subwoofer to taste. I would also recommend using the internal 1050 test tones for set-up on all channels except the subwoofer. The subwoofer test tone is just wrong and I think that's been documented before by Outlaw.
Concerning the subwoofer adjustment and the direct input, the subwoofer will only put out any signal being sent directly to it from the player. So with the Denon, you will get any signal below 80hz if you have the bass management on the player engaged. You then have the choice of adjusting the level using the subwoofer trim on the 1050.
Hope that helps...