We all know about that dreaded gamma shift tag in quicktime. If I have encoded a movie into DNxHD externally of Avid that contains the tag will it import properly or do I have to remove the tag before import?
If one could actually manage "the tag" then all applications could actually deal with the "shifting". There is no tag control that I know of in Media Composer once the media is in the DNxHD codec. The media is already created, but you shouldn't see a shift.
Other codecs wrapped in QuickTime can have its levels changed via AMA by going to the source settings and you have a choice of expand, restrict or do nothing. Basically allowing you to change where the black and white points fall - either RGB graphic levels of 0-255 or SMPTE video levels of 16-235 (all in 8 bit speak). The histogram on the source settings page as two white bars to show you where 16 and 235 lie in the image. Adjust those settings accordingly. If you're going for broadcast, DVD etc, then 16-235. If web only, then 0-255 is fine, but make sure you manage the export later properly so you don't crush again by selecting RGB.
For my work, I keep everything SMPT 16-235 so I am ready for broadcast, then export with RGB (expand) for web deliverables. Easy to keep track of. Only if you go back and forth with After Effects and stuff will you need to keep track of those levels.
What I hear from all the developers is that QuickTime tries to make it look good and will "try" to interpret from the codec metadata (not the wrapper) as to whether it is graphics levels, video levels and such. But it doesn't do it well and there are differences between QuickTime Player 7 versus the more consumer oriented QuickTime X player (use v7 - it's still in the OSX installer). What you point out is a tool that compares (like Avid auto-color Correct) black and white point levels to bring two shots the same. I do this all the time by shooting a chart and having the digital version in the MC and use the color match to bring them into what it should be under the keylight.
But when creating DNxHD essence outside MC and it is wrapped in QuickTime, the look is already baked in and you shouldn't see any shift when bringing that into MC.
And the transcoded version and what you see in MC should be the same. The difference you are seeing is how the application you used to do the transcode "interpreted" the settings. If you look in the QuickTime settings you will see radio buttons for RGB and 709. Not to mention that Canon 5D Mark II is RGB with NTSC color space... as an example of codecs and differences therein.
I would suggest linking to the file via AMA and seeing what the histogram shows. Make sure the shot has the blackest black and the whitest whites so you can see the whole range. And some cameras, with their gamma settings can change those levels as well, that you need to keep track of. Here is a chart I did for the original Panasonic DVX100 when it first came out and you could change pedestal in the settings which affected the recorded black level. All values were checked with footage shot with lens cap on (black).