Yes, you're right when you're using Enhanced Detection we are not updating the video.ffsplit in the comskip logs directory. We are rewriting the .edl file next to the recording if that option is enabled. Would you be interested in moving your scripts to use the .edl file?
You can even use a bash script such as this to convert an .edl to an .ffsplit:
awk -F'\t' -v prev=0 '
$3 == 3 { if ($1 > prev + 0.5) printf "-c copy -ss %.3f -t %.3f segment%03d.ts \n", prev, $1 - prev, n++; prev = $2 }
END { printf "-c copy -ss %.3f segment%03d.ts \n", prev, n }' "$1"
I'm struggling to tease out exactly what your saying your issue (2) is, but we'd need diagnostics to understand it more.
Unfortunately it's very hard to calculate that, because it only does the work when the system is idle (not recording, not playing, not doing other tasks that are higher priority). I'd need to see diagnostics from your server after some processing to even guess how long it will take. You can see the pending number in the web interface, and by looking at it over a day or so, would be able to project a very general estimate.