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I just want subtitles passed through from source to output, as would be expected for a sane default.

Under Config>Automation>Passthrough Streams I have Subtitles checkedboxed

The problem is it extracts .sub, .srt, .idx files all over the working folder, and Hybrid doesn't delete them when finished.

Am I doing something wrong here?

Since Hybrid only has basic subtitle support, it does not delete subtitles by default.
(+ I usually use subtitles mainly to add some 'watermark' and use the same subtitle file for tons of files. )
If you enable "Subtitle->Import->Delete subtitle after muxing" and save that in your defaults, or enable it before loading your files, Hybrid should delete the subtitles.

Cu Selur