Default Subtitles

[Host-in-the-Shell]

I believe the reason why external subs are preferred is because they can avoid transcoding and, by extension tone mapping, which can be taxing on server hardware and outright incompatible with certain clients.

What you can do to avoid downloading misaligned subs is to edit the library (for say, movies or tv shows) in your server's dashboard, and under subtitle downloaders, select the option labelled "Only download subtitles that are a perfect match for video files".