mkvmake pulls the Forced flag from its source, so it’s likely that your DVDs have a set flag for certain subs. You can use mediainfo to check this on your mkv files.

Mkv is simply a container format, which means you can probably unset the forced flag with mkvmake directly without having to unpack all the streams and remux them.

Handbrake is amazing, but it does have a LOT of controls, so there’s only so much hand-holding it can do when you start looking behind the curtain of how av files work.