The reason matomo threw a 500 error was, indeed, AddHandler.
In my virtualhost for the WP website I had AllowOverride limited to a few fields, namely “Limit Options FileInfo”, as that is the default behavior of a new WP install. Adding “AuthConfig” to this list allowed matomo to work properly.
The diagnostics page still shows a warning, this seems to not be effecting the plugin’s functionality.
Issue resolved.
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