Are you still using HandBrake? Try to demux and mux using MKVToolNix as well. (If only track has 98% size then MediaInfo estimates mkv container overhead to be the remaining 2%.)
Basically, just keep turning knobs until you have something that works. Try x265cli instead of HandBrake. Try lower level, lower resolution. Try without HDR and UHD-BD options etc.
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