03.09.2021, 21:00
I can't reproduce version problem anymore
Seems problem was fixed somehow in newer versions of Hybrid
Checked this:
Deleted ~/Library/Application Support/Hybrid folder
Renamed MKVToolNix-53.0.0 to MKVToolnix.app and replace with it MKVToolnix.app inside Hybrid contents.
"Config->Tools->Clear all cached tool infos"
trigger "Config->Tools->Tool Versions"
Known Tool versions window is empty. (Guess Hybrid need one more restart here)
Checked "Config->Profiles->Auto Save defaults".
Restart Hybrid
trigger "Config->Tools->Tool Versions"
Known Tool versions window show all tools versions now, including proper MKVToolnix versions.
mkvextract: 53.0.0
mkvinfo: 53.0.0
mkvmerge: 53.0.0
No error during MKV muxing.
Also checked simpler way like this:
Deleted ~/Library/Application Support/Hybrid folder
Renamed MKVToolNix-53.0.0 to MKVToolnix.app and replace with it MKVToolnix.app inside Hybrid contents.
Checked "Config->Profiles->Auto Save defaults".
Restart Hybrid
trigger "Config->Tools->Tool Versions"
Known Tool versions window show all tools versions now, including proper MKVToolnix versions.
mkvextract: 53.0.0
mkvinfo: 53.0.0
mkvmerge: 53.0.0
No error during MKV muxing.

Checked this:
Deleted ~/Library/Application Support/Hybrid folder
Renamed MKVToolNix-53.0.0 to MKVToolnix.app and replace with it MKVToolnix.app inside Hybrid contents.
"Config->Tools->Clear all cached tool infos"
trigger "Config->Tools->Tool Versions"
Known Tool versions window is empty. (Guess Hybrid need one more restart here)
Checked "Config->Profiles->Auto Save defaults".
Restart Hybrid
trigger "Config->Tools->Tool Versions"
Known Tool versions window show all tools versions now, including proper MKVToolnix versions.
mkvextract: 53.0.0
mkvinfo: 53.0.0
mkvmerge: 53.0.0
No error during MKV muxing.
Also checked simpler way like this:
Deleted ~/Library/Application Support/Hybrid folder
Renamed MKVToolNix-53.0.0 to MKVToolnix.app and replace with it MKVToolnix.app inside Hybrid contents.
Checked "Config->Profiles->Auto Save defaults".
Restart Hybrid
trigger "Config->Tools->Tool Versions"
Known Tool versions window show all tools versions now, including proper MKVToolnix versions.
mkvextract: 53.0.0
mkvinfo: 53.0.0
mkvmerge: 53.0.0
No error during MKV muxing.