I also keep just the .ts files for all recordings, which I will play "soon" and then delete, and Kodi plays that just fine. For anything I want to store for longer periods, and therefore look for a smaller file, I use this ffmpeg command in a Python script, started manually:
# HandbrakeCLI options:
# -O, --optimize Optimize mp4 files for HTTP streaming ("fast start")
# --preset "Normal"
# + Normal: -e x264 -q 20.0 -a 1 -E faac -B 160 -6 dpl2 -R Auto -D 0.0 --audio-copy-mask aac,ac3,dtshd,dts,mp3
# --audio-fallback ffac3 -f mp4 --loose-anamorphic --modulus 2 -m --x264-preset veryfast --h264-profile main --h264-level 4.0
#command =
'/usr/bin/HandBrakeCLI --preset "Normal" -O -i "' + fname + '.ts' + '" -o "path/' + fname + '.mkv" </dev/null 1> path/handbrake.log 2> path/handbrakeERR.log'
fname is the filename of the video without extension
Not sure how it deals with de-interlacing, but I think this is taken care off in Kodi anyway? At least, it works fine with me from DVB-S(2) recordings.