While I am unsure if this is possible at the moment for ManageWiki. I do feel like adding the ability to modify $wgHiddenPrefs and $wgDefaultUserOptions via ManageWiki could be incredibly beneficial and useful.
I have resigned from SRE. I am no longer handling extensions for Miraheze right now. But to answer your question I already added $wgHiddenPrefs to ManageWiki a while ago, but $wgDefaultUserOptions is unfortunately still impossible as far as I know.
I resigned yesterday. Its impossible because of the complex structure of $wgDefaultUserOptions, since each key as a preference and each value can be a different type of variable, there isn't really an ideal way to implement it into the UI in ManageWiki. It could be a new field for every possible preference but that would not be good on UI either. Apologies that it isn't possible, and hopefully that this answered your question a bit.
Not really from a UI perspective. It's kinda hard to explain for me, but it really can't be done, unfortunately. Though like I said, I don't handle extensions anymore, at least not for now, so I cant say if it'll ever be attempted or not right now. I agree it's useful, and it would be very nice to have, but unfortunately can't right now as far as I know.