I'm on a project right now where I'm using FFMPeg.
It turns out that for the Apple stuff it loses a lot of color information. Compressor captures this color information by using ICC profiles that it generates from (the quick time headers of?) a .mov file in non obvious ways. Gamma, contrast, and chroma are lost in transit.
This is perhaps not a huge deal since we're dealing with a proprietary file format anyway, but it does mean I had to stop using FFMPeg in the project, which was a shame.
I worked with ffmpeg for a few years about 6-7 years ago. If I learned anything from that time period, it's that whenever I started a sentence with "ffmpeg doesn't do ..." I was wrong. It may not do it out of the box, and the way to do it may not be documented anywhere, but I was always wrong.
This is probably the most complicated part about ffmpeg. It does EVERYTHING. However, much like the tar command, it takes a lot of googling and doc digging to find the right magic combination of flags and settings to make EVERYTHING happen.
That's not really a knock on it, ffmpeg has some pretty reasonable defaults all around. However, there's a billion codecs and use cases that make it's job challenging.
I'll agree, ffmpeg is super powerful, but here is a situation where I just couldn't get it working:
How do I take a sequence of 5000 pngs, apply a 5 frame crossfade between each one, and then output the resulting mp4 ?
I spent days on trying to figure it out, and in the end I had to generate the xfade frames with imagemagik, then I had to split the rendering into separate mp4s and stitch them together.
I just couldn't get it to slurp in a big list of files and do the filter all in one go. I can't exactly remember what went wrong when I tried to ask it to render the ~25000 frame from imagemagik.
I guess this fits your definition of "not do it out of the box".
This will take longer obviously but a two step process where you export to an image sequence (like say 16 bit tiff) is a pretty fool proof way to retain colour information. And true pro industries like the VFX industry pretty much exclusively use image sequences (because they are just superior in everyway). Although they would be using either DPX or EXR sequences.
It turns out that for the Apple stuff it loses a lot of color information. Compressor captures this color information by using ICC profiles that it generates from (the quick time headers of?) a .mov file in non obvious ways. Gamma, contrast, and chroma are lost in transit.
This is perhaps not a huge deal since we're dealing with a proprietary file format anyway, but it does mean I had to stop using FFMPeg in the project, which was a shame.