Well, it has to be possible, since ffmpeg wrappers/GUIs like Avidemux do it. The question is, do you have to write your own batch file or can you do it in a single command? And I'm honestly not sure. I'd like to know myself actually. I tend to do the same as you do, but if it's too many (or too high resolution) segments, I've so far taken the lazy route, and just took the quality hit and double time investment and encoded it in one of the codecs Avidemux offers (usually libx264 with a crf=20 or lower to preserve quality), before going over it with ffmpeg to transcode it into whatever obscure codec I actually need. If you only cut at keyframes, you don't even need to re-encode at all with Avidemux. Webm related for a short demo I did for an encoding tutorial a few years ago.
Doing it in ffmpeg alone would be sweet though. Would definitely require a complex filtergraph. The seeking is the main problem, so you can't just use overlays. Have you tried the movie filter as a multimedia source?
http://ffmpeg.org/ffmpeg-filters.html#movie-1It claims to offer seekpoints. So maybe you could start with the first segment with -ss and then constantly overlay (with the enable='between(t,[st],[e]) parameter) additional segments with a giant filtergraph? I've so far found it too daunting to try, but I've wanted to figure out the whole "resetting PTS for multiple streams" business for a long time, which seems to be an integral part according to the examples in the documentation.
But at this point it might honestly be easier to write your own batch files.
