As it says on the tin. The important thing to do here is to make Special:ManageWiki automatically update both wiki_settings and the other wiki_* values, immediately after the population is done.
During the population process, Special:ManageWiki should be read-only.
Actually, screw this. wiki_private and wiki_closed are currently written to all.dblist, and the wgConf values for the private/closed status are always populated: https://github.com/miraheze/mw-config/blob/master/LocalSettings.php#L3149
Depending if this is needed (e.g. SiteMatrix - although that extension uses private.dblist and closed.dblist, so we can keep those dblists), we will have a problem here, as it means we'll have to loop through all CDB lists to fill the wgConf array...