Edit: oh, and furigana can be done in AegiSub by making a new line, changing the font size, then dragging the line into place in the video preview pane.
When I looked at this problem earlier, I considered something very much like that (but using SRT and scripting because I like to keep content and style separate, similar to HTML and CSS). I was never satisfied with the appearance of the Furigana unless I was able to customize the tracking (inter-character spacing) and positioning, so that they would better align with the words they applied to, and that was really hard (not impossible, I’m sure) to automate. So when I found out I didn’t need to bother with Furigana, I happily dropped all attempts to make it happen. Similar to my short, doomed experiment with vertical Japanese subtitles.
There’s a lot of things I try out for this project that never see the light of day. But the only one I feel regret about not doing is the Malayalam subtitles. Most of the time it’s more like: I came, I saw, I decided that wasn’t a very good idea after all. But Malayalam… I’m probably going to revisit that and fail another four or five times before I give up.
But back to the original topic. I do maintain theatrical subtitles for the burnt-in Jabba and Greedo subs, but only if I know those were on the original 35mm prints and I know their font/size/placement (what’s the point of just text?). For these Japanese subtitles, I don’t know any of that.