This is pure speculation, but as a thought exercise to explain things it has value.
Consider that the unit was opened, it may likely have been returned to the store.
The previous owner ran the setup routine (which includes Audyssey).
The previous owner had very efficient speakers (let's say 103dB).
This would cause the AVR to set the relative level very low so as not to blow you out of the room (which seems like a decent reason to not have the test tone at a fixed level?).
The store doesn't do anything to the AVR. The previous owner says it works fine, he just decided he didn't need it, so they put it on the shelf as a open box unit.
Now you bring it home and set it up with less efficient speakers (say 85dB) and the volume is now 18dB below the optimal level set by/for the previous owner's speakers! In this condition your adjusting the AVR to +12dB would still be 6dB shy of "optimal" (as determined by the setup routine).
Assuming there is a modicum of reality in the above scenario,
1) You really should return the AVR to its default settings. There are so many "nooks and crannies" in the setup menus, it is simply best to start with a clean slate to make sure there are no errant settings from the previous owner. Note this will also reset time/phase/distance matching of the previous owners speakers. (Seems like the default is to assume all speakers are 11 feet away so they are all in sync without customizing to your layout).
http://manuals.denon.com/AVRX4400H/EU/EN/GFNFSYvyalrwrt.php
2) Run the setup routine. After a reset, it will automatically suggest this. You can skip it, but I can't think of a reason you would. If you do not believe in Audyssey, you can turn Audyssey off, but you will retain the level matching and the time/phase matching of the setup routine.
I understand you may not have time or want to run Audyssey before the installer puts in the speakers, but the reset is quick and returns everything to the defaults which are chosen as "non-problematic neutral settings". Things won't yet be "optimized" as Audyssey is supposed to, but having someone else's settings is a "worse than non-problematic neutral" situation!