At present when we add a new wordpress installation for all including the clean wordpress installtion. technically this will not affect the site however. when we use a security plugin it will be flagged. for example in Sucuri plugin it will be flagged as Core WordPress Files Were Modified. (this file flagged by all security plugin ). f someone delete it by mistake they will get 5xx error untill they fix it. to fix it they will have to add the file using SFTP. As this file can be deleted with wordpress security plugins like Sucuri