If you need to export ProRes, first do a transcode (or video mixdown) of your sequence to ProRes _inside_ Media Composer, then export Same As Source.
If you do a Custom export in MC, you are using the QT encoder, and you will then be using either the Apple H264 QT codec or the Apple ProRes QT codec, both of which are notorious for gamma shifts and automatic black level corrections. The codec as used inside MC works fine. Also, it will be much faster than using the old and slow QT engine to transcode.