MKVextract/merge and Aegisub seems to be doing the trick. I'm just perfecting adjustments for the default track before applying it to all files.

I was also able to change the default language priority, but once I started using merge, I found it easier to just remove the unnecessary track(s).

Given that I'm pretty bad at making comparisons, and just out of curiosity, what settings does Gotwoot normally use for subtitles? I'm trying to figure out if doing pure white, or a more cloudy color would work better for the text, but I think I have the outline color picked. I'm not sure what the secondary color refers to, and I assume the shadow is best at black. But what about the thickness of the outline and shadow?