I've a issue with emby that the playback of files in a browser isn't possible after updating to version 126.96.36.199 by using your method with the apt tool plugin. The update works but it seems that emby has a new installation procedure which currently not properly work with the apt tool plugin. This causes to me that ffmpeg isn't available anymore and needs to be installed manually. The admin luke of the emby media forum asked me who is maintaining the apt tool plugin to get in contact and get their support to migrate the new package to apt tool.
I hope you're the one to contact regarding apt tool plugin or maybe can point me to the right person.
The apt tool plugin doesn't do any magic. It just executes the apt-get install or dpkg -i command that a person would execute from the command line which seems to be exactly what the instructions recommend here. If it is an interactive installer and some questions don't get answered, I can see it having issues. But, I am not going to change the apttool plugin to do something special for emby. I would say use docker if this is the case.