I am not 100% sure what kind of “commentary” this relates to.
In the case of flagging the content of a stream as being a “commentary”-type of thing:
If I use the GUI version of MKVtoolnix, I can add the “commentary” flag on subtitle and audio streams without them causing crashes in Plex.
I have used this for the last 2–3 years when adding new items, without issues. It is ingested into the Plex DB and appears in the Plex media info. Just as the regular flags for “original language”, “hearing impaired”, and “visual impaired” do.
<Part accessible="1" exists="1" id="1283804" key="/library/parts/1283804/1773503301/file.mkv" duration="5581674" file="J:\Filme4\Rushmore (1998) {tmdb-11545}\Rushmore (1998) {tmdb-11545}.mkv" size="5879582945" container="mkv" deepAnalysisVersion="6" indexes="sd" requiredBandwidths="16463,13398,11257,10118,9684,9305,8649,8649" videoProfile="main">
<Stream id="2191911" streamType="1" default="1" codec="hevc" index="0" bitrate="7787" language="Englisch" languageTag="en" languageCode="eng" bitDepth="8" chromaLocation="left" chromaSubsampling="4:2:0" codedHeight="816" codedWidth="1920" colorPrimaries="bt709" colorRange="tv" colorSpace="bt709" colorTrc="bt709" frameRate="23.976" height="816" level="120" profile="main" refFrames="1" requiredBandwidths="10809,7895,5820,4793,4349,3970,3261,3261" width="1920" displayTitle="1080p" extendedDisplayTitle="1080p (HEVC Main)"> </Stream>
<Stream id="2191912" streamType="2" default="1" codec="aac" index="1" channels="2" bitrate="221" language="Deutsch" languageTag="de" languageCode="deu" audioChannelLayout="stereo" profile="lc" requiredBandwidths="222,222,222,222,222,222,222,222" samplingRate="48000" displayTitle="Deutsch (AAC Stereo)" extendedDisplayTitle="Deutsch (AAC Stereo)"> </Stream>
<Stream id="2191913" streamType="2" codec="ac3" index="2" channels="6" bitrate="448" language="Deutsch" languageTag="de" languageCode="deu" audioChannelLayout="5.1(side)" requiredBandwidths="448,448,448,448,448,448,448,448" samplingRate="48000" displayTitle="Deutsch (AC3 5.1)" extendedDisplayTitle="Deutsch (AC3 5.1)"> </Stream>
<Stream id="2191914" streamType="2" selected="1" codec="aac" index="3" channels="2" bitrate="221" language="Englisch" languageTag="en" languageCode="eng" audioChannelLayout="stereo" original="1" profile="lc" requiredBandwidths="222,222,222,222,222,222,222,222" samplingRate="48000" displayTitle="Englisch (AAC Stereo)" extendedDisplayTitle="Englisch (AAC Stereo)"> </Stream>
<Stream id="2191915" streamType="2" codec="dca" index="4" channels="6" bitrate="4276" language="Englisch" languageTag="en" languageCode="eng" audioChannelLayout="5.1(side)" bitDepth="24" original="1" profile="ma" requiredBandwidths="4667,4521,4382,4274,4274,4274,4274,4274" samplingRate="48000" displayTitle="Englisch (DTS-HD MA 5.1)" extendedDisplayTitle="Englisch (DTS-HD MA 5.1)"> </Stream>
<Stream id="2191916" streamType="2" codec="ac3" index="5" channels="2" bitrate="192" language="Englisch" languageTag="en" languageCode="eng" audioChannelLayout="stereo" comment="1" requiredBandwidths="192,192,192,192,192,192,192,192" samplingRate="48000" title="commentary" displayTitle="Englisch (AC3 Stereo)" extendedDisplayTitle="commentary (Englisch AC3 Stereo)"> </Stream>
<Stream id="2191917" streamType="3" canAutoSync="0" codec="srt" index="6" bitrate="0" language="Deutsch" languageTag="de" languageCode="deu" requiredBandwidths="1,1,1,1,1,1,1,1" displayTitle="Deutsch" extendedDisplayTitle="Deutsch (SRT)"> </Stream>
<Stream id="2191918" streamType="3" canAutoSync="0" codec="srt" index="7" bitrate="0" language="Englisch" languageTag="en" languageCode="eng" requiredBandwidths="1,1,1,1,1,1,1,1" displayTitle="Englisch" extendedDisplayTitle="Englisch (SRT)"> </Stream>
<Stream id="2191919" streamType="3" canAutoSync="0" codec="srt" index="8" bitrate="0" language="Englisch" languageTag="en" languageCode="eng" hearingImpaired="1" requiredBandwidths="1,1,1,1,1,1,1,1" displayTitle="Englisch SDH" extendedDisplayTitle="Englisch SDH (SRT)"> </Stream>
<Stream id="2191920" streamType="3" canAutoSync="0" codec="pgs" index="9" bitrate="55" language="Englisch" languageTag="en" languageCode="eng" hearingImpaired="1" requiredBandwidths="90,90,90,90,90,90,90,90" displayTitle="Englisch SDH" extendedDisplayTitle="Englisch SDH (PGS)"> </Stream>
<Stream id="2191921" streamType="3" canAutoSync="0" codec="srt" index="10" bitrate="0" language="Dänisch" languageTag="da" languageCode="dan" requiredBandwidths="1,1,1,1,1,1,1,1" displayTitle="Dänisch" extendedDisplayTitle="Dänisch (SRT)"> </Stream>
</Part>
But maybe I have missed it, if here is another type of commentary flag in the MKV spec.
The issue might also be connected to whether this is a regular MKV flag, or an XML-based flag. I made it a habit of removing all XML flags from my MKV files before adding them into my library. Because these can at times contradict the flags and language definitions of the legacy MKV flags.
XML tags appear like this in the GUI version: