DCP-o-matic 1.x will only create burnt-in subtitles, not the 'common' XML/cinecanvas subtitles used by commercial mastering software. That means, the subtitles will need to be overlayed to the individual frames and be encoded during the J2C conversion process. As long as it stays like this, it makes little sense for a versioning process, as the CPL with and without the subtitles both will need to carry their full individual video file, which is 90% of the storage space. So, aside from a 'nicer' package to show up in the ingest window, currently there is little to gain with it, aside from some space saving for the audio file. So, the only method so far is to create two OV packages, one with, one without subtitles.
Of course, sooner or later versioning will be a necessary and nice option.