How to batch cut a folder of videos with a list of timestamps
You almost invented EDL files. It can be rendered with almost any NLE editor.

If you want cut out part of file, you can use ffmpeg:

     ffmpeg -ss 3:00 -i file.mp4 -t 1:01 -c copy file_00300_00401.mp4


As you can see, here -copy option, so cut points will be only on keyframes. No quality loss. If you want more precise, you must reencode whole video (and possible move -ss option after -i)

To achieve your text format/file naming style, you must write script in any language. Just parse input data and paste it as ffmpeg's options.