DVD subtitles can be built as either one track for all formats or 2 separate merged tracks where one is automatically activated for WS and the other LBX.
The thing is, if you are using a program like BDSup2Sub you are working with a specific version.
In other words when you rip the tracks from a DVD the tracks rip separately and need to be resize and/or retimed separately.
Seriously, I will dig into this more next week. This is a terrible weekend for me.
I'm also thinking of making another important change: converting the guide to use Eac3to. It's a lot more direct for a lot of the audio conversions and is fairly mature.
Except for audio tracks where you need SoundTouch, it's can do everything else including DTS conversions and slowdown in one step.