It affects the public perception, and facilitates misleading the public. Whether or not that is a practical difference depends on whether one is measuring the political outcome or the legal outcome.
The FBI has no reason to render a report unless its investigation produces evidence that supports finding probable cause that a crime has been committed.
The public is being conditioned to view an FBI report that does not recommend indictment, as clearing the target of the investigation.
I haven't looked hard, but I don't think the FBI issues reports on investigations that clear targets, that lay out facts and then say "but these facts don't amount to probable cause a crime has been committed."
"Attorney General Loretta E. Lynch plans to announce on Friday that she will accept whatever recommendation career prosecutors and the F.B.I. director make about whether to bring charges related to Hillary Clintons personal email server, a Justice Department official said." (Emphasis supplied).
My scenario is, of course, conditioned on the assumption that there will be a "recommendation" for proceeding against Hillary.
I quite agree with you that if the report does not recommend prosecution, Hillary will cite it just as she has cited the Benghazi report claiming it as an exoneration.