$wgExtensionFunctions is an odd special case that behaves like a hook, but not quite. It could easily be deprecated and replaced with a hook. Migration of extensions that currently register ExtensionFunctions would be trivial.
Note that $wgExtensionFunctions are called late in Setup.php, after MediaWikiServices is initialized. There even is a hook called earlier, namely the SetupAfterCache hook. Adding a SetupComplete hook to replace $wgExtensionFunctions would be trivial.