I don't know that Gaiman is here to clean up anything (Morrison's back in June, after all); he's just using the "death of Batman" to tell a metafictional story about the Bat-mythos (which is one of his two primary story setups; the other is "people find a secret magical world").
was kind of a manifestation of Morrison's worse tendencies: on an allegorical level, which is his primary concern, you can see how it all fits together if you puzzle over it. It's successful as metafiction, but not as fiction, in part because Morrison is intentionally obstructing the frame in the service of his metafictional end. Final Crisis
is basically doing two things: there's the Fifth World stuff (which is an absolutely fantastic concept; Morrison isn't short on those), which is a fairly straightforward genre story, and then there's the Mandrakk/metafictional stuff about the ur-hero, which is mainly in Superman Beyond and then arrives in the last half of the last issue, and is rather less successful.
Also, I think fan expectations of RIP got mixed up by Final Crisis'
marketing, since it was basically just supposed to be Morrison's treatise on Batman as the Ultimate Human, which was then followed by the death stunt, otherwise unrelated to RIP itself.