History and storytelling are a complicated pairing with all three of these writers, and I'm glad you pointed that out. I see a few different things going on at once...
There's the obvious 'theory' comment, sort of Jamesonian, that history as we know it is a constructed narrative anyway, the whole hiSTORY thing, so by telling histories like stories we both cloak them in drama and, possibly, reveal how constructed they are. That's the bare-bones approach.
The genre approach is to ignore 'real' history for a moment, and look at G, M, and E's retellings of fictional histories, rewriting the high-fantasy universes of superhero comics. They've all done it, in direct and indirect ways. Gaiman does a fantastical trip through the DC universe in the prequel to Books of Magic that tells the fantastic history IN TERMS OF its metaphorical power, not its concrete detail. His retellings are critical interpretations, maybe even analyses, of narratives.
Moore's work on this has been more indirect, in analogue heroes mostly. Almost all of his superhero work does it. In order: Marvelman, Watchmen, 1963, Supreme, and Promethea. Interestingly, he seems to work backward, stylistically, from Marvelman to Supreme, starting with so-called revisionism (Marvelman, Watchmen), in which heroes are placed into not the 'neverwhen' version of the present, but the actual present world, as much as possible. Then 1963 does the Marvel age (with really charming results), and then Supreme revisits the whole history of Superman, from end to end. Promethea does something similar, come to think of it, but with Wonder Woman, creating a version of her in the present and then slowly revealing her whole history.
The extra thing in Promethea, the conceptual payload if you will, is its demonstration of a subjective/sensory model of reality as we know it. The ending (can't recall if you've read it, so I'll only speak of it in abstract terms) shows us that the world just is perception, that so-called objectively provable facts are, themselves, merely the results of more perception. To change perception, to change subjectivity, just is to change the world. That, as far as I can tell, is Moore's theory of what 'magic' actually is, manipulating perception, usually with words (spells, grimoires, the bastardization of Latin in 'hocus pocus' and 'abra kadabra,' etc.), but just as easily, maybe more so, with pictures.
If reality just is perception, then history is another technology of perception, of memory. Every new version of a moment in history, fictional not, is just another perception. Equally 'real,' perhaps, but not equally powerful, and that's where the heavy lifting comes in. I can't just wake up one morning and decide the world is different than everyone else sees it, and then expect everyone to come there with me to that new world. Shifting perception is extremely difficult with entrenches ideas, entrenched perceptions and subjective beliefs, especially when they pretend to be objective beliefs and facts, but actually doing that work, actually shifting perceptions, is what Moore calls 'magic,' and it's the work of the historian as much as the storyteller, as well as scores of others, of course.
Then there's Ellis, whose stories very strongly advocate truth, objective and verifiable. Transmet and Planetary are all about revealing truth that has been obscured by rhetoric. The Beast is an honest monster, but the Smiler hides the teeth of a predator in plain sight, in an expression of friendship (if I may get a little poetic, for a moment). The Planetary manuals, history texts, are set up in diametrical opposition to The Four who (it will be revealed later, spoilers!) have been screwing with the path of commerce and technology for quite some time in the Wildstorm universe, creating a new world based on their own perceptions, perhaps? Their version of Reed Richards (The Four are The Fantastic Four, of course) lays mental eggs inside people's brains and controls their perceptions. He wipes Elijah Snow's memories because he gets too close to 'the truth,' and Elijah has to reconstruct it through evidence and his own Planetary books. In both series, text is trustworthy, verifiable, objective, whether in digital form or not (Spider's live column at the end of Back on the Streets, for example, is just letters from 'the feed'). Pictures are granted the respectability of journalistic truth, too; Spider constantly snaps pictures with his glasses, and the pics that accompany his live column at the Transient riot are easily as inflammatory as the text.
Transmet, unlike Planetary, reveals something of the slipperiness of perception in its narrative ploy of displaying the horrifying in order to reveal its beauty, thus demonstrating primarily our own preconceived notions of morality, but secondarily that perceptions rule morality, not eternal, concrete rules. Of course, there is still at least one, big, rule-based ethic at the core of both books, Truth itself. I think Transmet is similar to the post-colonial call for materiality that often positions itself in opposition to post-modernism and post-structuralism. "Fuck all of this fucking around with ideas and perceptions and pay attention to what's right in front of your fuckin' eyes, the atrocities, the indignities, the bleeding babies scorched Earth." Such an argument cannot afford to get caught up in epistemological questions like 'How do you know what the truth is?' or 'By what criteria can you verify it?'
Lastly, I have another idea that might apply to Moore and Gaiman only, that by injecting history with a healthy dose of fantasy, they do what fantasy usually does, they literalise metaphors and reveal/produce the conceptual meanings; essentially, they turn history into the kind of poetry that has to lie to the tell the truth. Gaiman and Moore paint pictures of drab, mundane worlds that have hidden fantastic ones sitting above or underneath them, as in Sandman and Promethea (the high-tech world that Sophie/Promethea lives in is, nevertheless, played up as a regular American city in the late 90s), and quite literally so in Neverwhere. The fantasy of London Below, for example, contains metaphors that 'read' London like a text, showing us an actual Angel of Islington, and Black Friar's populated with actual friars who actually wear black. Moore has a wonderful spoken-word piece where he does a conceptual walking tour of London, moving from place to place, revealing the city's history that is all around Londoners all the time, but which has disappeared because it's always in plain sight.
That got a little poetical. What I mean is that fantasy and science fiction present literal metaphors of human life in order to comment on it, wittingly or not. By placing such metaphors next to realistic depictions of the real world, they can work quite directly, as in Buffy, in which a teenager's feelings of fear and wonder at growing up are presented as actual monsters and saviours. That effect is distinctly different when there's a real world right next to a fantasy world. Come to think of it, that's a major part of the power of the superhero genre, which is almost always set in a contemporary world that is basically the same as our own, accept with added superheroes, like a prize in a box of otherwise boring cereal flakes.
The basic conclusion, I think, is that Gaiman and Moore are primarily interested in metaphorical perceptions, including perceptions of history, whereas Ellis generally sides with imperialism (though rationalism is rarely invoked, come to think of it), though Ellis has his hand in metaphorical perception, too, being a storyteller, after all.