The new version is working fine with Vector skin, keeping the dark mode across pages, but there is a regression on my wiki: it does not work anymore with Chameleon skin. It used to work before with both skins.
Topic on Extension talk:DarkMode
It seems Chameleon does not give footer links IDs, so there's no simple way to add listeners to them. We'll have to either come up with a hack, or make the placement of the darkmode toggle configurable. I think the latter is a good idea anyway. I'll look into this soon.
Other skins meanwhile seem to give footer link different IDs, so either way you have identified a cross-skin compatibility issue.