Nevertheless, I would still strongly recommend using Handbrake or something else that uses x264— that's the best H.264 encoder. x264 has good presets for various speeds/qualities, or I could help you optimize the settings for this type of content if you're interested.
Handbrake has a CLI in addition to the GUI, ffmpeg is another good CLI option.
Yes, I've tried both Handbrake and ffmpeg (and mplayer), and spent a lot of time tweaking the settings. I prefer MPEG Streamclip for this process—its ability to add new files to the queue after I've already starting the encoding process is particularly useful. Handbrake sometimes chokes on the DVD files generated by the legislature (I have no idea why), which is a dealbreaker For basically any other video encoding/decoding task, I use ffmpeg or mplayer Thank you, though!
I don't understand why you have to upload the videos. Is there a part that requires a ton of processor power? It seems like you could install the right packages on the Mac, or just start a Linux VM on it.