What are the benefits of a CLI encoder (e.g. FFmpeg) over GUI Software?
You have 10,000 videos that need to have a logo overlayed, subtitles burned in from srt files, and a standard copyright notice attached to the end. Then you need to make three different versions of each, at different sizes and codec settings. It's a quarter to five on Friday night.

Option 1, you spend all weekend doing it in a GUI app, and you have no life.

Option 2, you do it with ffmpeg, which can do all these things, you spend fifteen minutes setting up a CLI batch encoding script, and as the big hand points to 12 you leave it running and head for the pub.