If you are OK with longer render times I would try switching to Constant bitrate around 45 to 60. I like 25 for most projects. Another trick you might try is symlinking the .C4D project file in after effects. This way you are only compressing the composition once, inside media encoder. As much as I love the prores codec you might want to try .h264 mp4. In most cases It’s going to require a lot of trial and error depending on the project. What I like to do when I’m test rendering options is only render out a couple frames of the more complex part. If I like what I see, I save the preset and render the entire project.
File Format: .mp4
Codec: .h264
Bitrate: 45 cb/s
Framerate: 24fps
Hopefully I was able to help. Good luck on the project