I was editing my last post just as you replied. I was going to add that when using the native Cineform encoder, setting the YUY2 output explicitly for Rec709 is accurately reflected in the comment 'Using conversion YUV420-709 ->YUYV-709'.
On the other hand, transcoding (these YUV420-709 inputs) to MagicYUV-YUV420 (configured for Rec709 YUV420 input) does not require specifying 'Rec709' in the output pixel format. Leaving at default 'Same as Decoding' (YUV420-709) works fine (pass-through with no black-coded highlights) provided you ignore the "(?) Format Not Accepted by Codec, YMMV" comment. Same with UTVideo YUV420. Well that's 'my mileage' at least
I won't bother posting any screen shots.
Cheers.