Heya -- are you talking about the setting for whether your own journal style defaults to site skin comments or journal-styled comments?
That's not in the customize theme area; it's in the user settings' "display" section, and its name is "Entry Page Default: Your Journal". Does that help?
As for bugs with journal-styled comment pages -- those work fairly well these days, but only if you're using a style that was designed for Dreamwidth (i.e. a "core2" style). If you're using a "core1" style imported from LJ or IJ, well, those have issues that no one has any plan to ever fix. (I don't speak for staff, but from the perspective of someone who does a bit of volunteer work on the site: There's MORE than enough work to be had improving our own stuff without chasing 1-1 compatibility with some other platform's theme system.)
Re: "Disable Custom Replies" ticky box is gone.
That's not in the customize theme area; it's in the user settings' "display" section, and its name is "Entry Page Default: Your Journal". Does that help?
As for bugs with journal-styled comment pages -- those work fairly well these days, but only if you're using a style that was designed for Dreamwidth (i.e. a "core2" style). If you're using a "core1" style imported from LJ or IJ, well, those have issues that no one has any plan to ever fix. (I don't speak for staff, but from the perspective of someone who does a bit of volunteer work on the site: There's MORE than enough work to be had improving our own stuff without chasing 1-1 compatibility with some other platform's theme system.)