We edit all HD footage in ProRes (HQ) in Final Cut, but would it be better to turn the 5D's H.264 to ProRes LT as the data rate is more than enough for the data rate of H.264? Or is there other disadvantages to using LT regarding quality and what about mixing HQ & LT in ProRes (HQ) timeline, I assume more rendering is required?
In my opinion there is never a need to use HQ as it just makes the file sizes too large wasting disk space, and there is no benefit you could gain when transcoding 5d footage to it. I would recommend following canon's suggestion that you use LT. If you do a side-by-side comparison of HQ and LT, do you see any perceptive degradation of the footage? I have not yet been able to, and as you say the data rate is more than enough, as we see here:
for the canon 5d-
HD bitrate is approximately 38 Megabits per second (4.8 Mbyte/s); and: The 21 megapixel sensor is
downsampled to HD resolution by only using every third line and 4:2:0 chroma subsampling
And since we also know the chroma sampling is a mere 4:2:0 what could you possibly gain? Now if I had a 2k image with full color sampling I might think of pro res 4:4:4 but then again the original footage needs to be captured at that kind of sampling from a camera that can actually do it.
As far as being in the same timeline, you should be able to mix all flavors of proRes 422 and not have to render except for final output.
Hope this helps.
ps- if someone can actually show me a visible difference you are welcome to try, or if you have scientific data to back your claim please let me hear it.