MCEBuddy does use MKVMerge with cluster-in-seek option when used with remuxto.
Simple answer, open the profile you are using. Say you are using ffmpeg, changeffmpeg-ext=.mkv
to
ffmpeg-ext=.mp4
and add
ffmpeg-remuxto=.mkv
This will cause mcebuddy to use ffmpeg to create a mp4 file and then use mkvmerge to create a MKV file with the following options:
"--clusters-in-meta-seek -o <output> --compression -1:none <input>"