Open the https://meta.wikimedia.org/wiki/Special:Preferences, I noticed that "MediaWiki:Email-allow-new-users-label" checkbox I have set as a global option but presented as a switchable blue after the page loaded. Before the page is loaded, all checkboxes are grayed out and inoperable. If I switch the set to local exception checkbox of the Email-allow-new-users-label box twice, the Email-allow-new-users-label box change to the correct gray.
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Things have probably changed since this was first reported (sorry for the slow response!) but it's looking like the bug might be even worse now: when I go to https://meta.wikimedia.org/wiki/Special:Preferences, none of the preferences with global values are disabled (and they all should be, with only the local-exception box enabled). It appears to be the same on all wikis.