To address this I would like to suggest that MakeMKV's default processing be altered to leave the CEA-608 Closed Captions in the user data in MPEG-2 video streams. Failing that, CCExtractor is capable of outputting to subtitle formats which preserve all caption information, particularly SCC and CCD, though those are somewhat niche formats.
EDIT: Unfortunately, CCExtractor does not preserve positioning information when converting to SubStation Alpha or any other more conventional subtitle format. Positioning info is only preserved in SCC, CCD, and the CCExtractor-specific formats like RAW and BIN.