Extensions need to not use class_exists to check if an extension is loaded, at least for extension classes that can be autoloaded without the extension being enabled. This might happen for extensions that have an composer generated autoloader and are handled by the composer merge plugin.
A replacement might be ExtensionRegistry->isLoaded('name') if the extension was converted to use that.
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I'm going to close this ticket because it is – as it is now – not actionable. What this needs at least is a list of the specific extensions that need an update. What this tickets description suggests might still be done, but can be done any time with new, more specific tickets.