Of course. Or Reaper could use mkvMerge in a native way to split videos. (Same way as it uses VLC and ffmpeg for preview) BUT! There is another problem according to mkvToolnix's splitting option. It allows timestamps only in chronological/sequential order. So if you make overlapping cuts you also get an error.
Anyway. VLC with mkvMErge and my extension is the best and most comfortable option at the moment.
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