Looking at the debug output, I see that
1. the SubtitleQueue has one entry
F:\temp\1_id_3_lang_en_default.idx:*,*:true:*,*:UTF-8:*,*:true:*,*:false:*,*:E:\1.mkv:*,*:true:*,*:false:*,*::*,*:false:*,*::*,*::*,*::*,*::*,*::*,*::*,*::*,*::*,*::*,*::*,*::*,*:false:*,*:auto:*,*:1:*,*:
2. Like configured the subtitle stream 'F:\temp\1_id_3_lang_en_default.idx' form that entry is embedded (= hard coded) into the video stream
=> seems Hybrid works exactly as you configured it
If you do want that the subtitle stream to not be embedded, but muxed into the container, do not enabled 'Config->Automation->Passthrough streams->embed first'.
Cu Selur