The logs are showing that the final MP4 contains all the media metadata. If it’s not showing on Plex then it’s likely a bug with Plex not reading it or processing it. You can use a third party tool like MP4 inspector to validate your final MP4.
We have provided an option for folks to use their own version of Comskip. If you’ve subscribed to Comskip and have access to the latest donator builds then you can use those instead of the bundled version. If what you have is working for you then you’re fine. You can check out the Comskip website for details on the new donator builds.