FWIW, if whatever authoring tool you choose doesn't accept BD-SUP subtitles, it's pretty trivial to convert them to BDN+XML with bdsup2sub. There's a sample command line to do this as a single batch process in the Project Threepio README if you still have it.

EDIT: Regarding burnt-in subs, alternate angles is ultimately the ideal way to handle subs for multiple languages while at the same time maintaining theatrical fidelity. Each language with theatrically-accurate subs could have its own angle, and the rest could get standard subtitles overlaid on a subtitle-free angle (more-or-less the same for the crawl, and even credits). But multi-angle is non-trivial, and besides I'd have to re-render most of my project :-/