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I would go the normal DGIndex->Avisynth->x264 route and make your softsubs using Subrip so you can set line widths before muxing (worst case, edit the longest line by hand, although I've never had this problem).
I realize this is inconvenient from the perspective of direct DVD->iPod using Handbrake, so if you can find a way to do your normal thing with Handbrake and rip softsubs separately with Subrip and then mux, I'd do that.
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