As SamuriHL pointed out, MakeMKV doesn't do any re-encoding of any kind.
Please consider adding a more universal sub conversion. I cannot see what the 'new' sub has brought to the party other than being difficult to handle for our multimedia toys.
Support for more than 4 colors for one track? And many other technical enhancements that I don't know about, but which are quite visible when you compare both subtitle formats.
VOBSUB (DVD) subtitles are a bit of a joke - for pure text tracks, converting Blu-Ray PGS subtitles to VOBSUB is feasible (though it doesn't look quite as good, it's readable and/or watchable), but as soon as it gets a bit fancier (e.g. Terminator 2 Blu-Ray subtitles), the converted subtitles look nothing like the original.
It's likely you're going to have to take the MKV and find a tool to convert the subs for you. Maybe Another EAC Gui will do it, but, I'm not really sure.
mkvextract + BDSup2Sub + mkvmerge should work. Not sure whether there's a good, up-to-date GUI for mkvextract though.