You can mux the subtitles in the same way you muxed in the new audio and then choose between them in the file. The reason I didn't do this is that many standalone players (including mine) don't support muxed in subtitles with mkv and some only support a limited number of muxed in subtitles (usually much more limited than the number of subs offered here) but vast majority, if not all, of the players capable of playing mkv are able to display subs if they're named the same as the videofile. It also saved me a lot of work, having to tag all the subs for the language they are in mkv merge.