As I stated only the original MOV will be affected by the 'Enable Final Cut Studio color compatibility' preference.
If one used compressor to convert to 4444 that transcoded file will ALSO be affected by that preference
If one uses other encoder/transcoder like AME or MPEG Streamclip those files will NOT be affected.
I think I know why.....
In the OS X Finder, select your original movie and also one converted to 4444 via Compressor,
hit command-i to open the information window. Below General you will find More Info... Un-hatch the arrow (if not already)
and look at the 'Color Profile'...... property.
It says: HD (1-1-1) when encoded to 4444 via Compressor
It says: (1-1-6) when checking the original coming from the canon
THAT 'Color Profile' property is simply NOT there on Adobe Media Encoder - encoded files.....
Look at the following screen shot....
Seems as if adobes encoder just voids that entry... Or what do I know ?????
Another funny thing....
If compressing to 4444 via Apples Compressor and I open the file in a Hex Editor and scroll to the bottom-end...
I can see that Compressor has recognized the file as Canon 5D MK II... It even states what version of the Firmware
was running as the movie was filmed.
All that information is NOT present in the AME encoded file.