I had luck with the alien subs in the black bars when I did my copy of Jedi (I was working backwards) and would highly recommend against them marring the image. I'd primarily object because it's possible to do the alien ones in the bars as they only come one line of text at a time. This effort seems focused on utmost quality so why spoil the picture if it can be easily be avoided? DVD subtitles can be set to coordinates corresponding to the black bars so it'll look fine.
After playing with a program called Subtitle Workshop (and others) I think the alien subs (and to a lesser degree the Closed captioned ones as they are sometimes more than one line) can be done properly in the correct font with overlay thus keeping the image pure. Which is the point, isn't it?