There are a lot of different 'facts' about the Warp, from a lot of different sources. When ships move through the Warp, they have the Gellar Field or they get torn apart. Right, ok, got it. But an Ork fleet can plunge into the Eye of Terror, disembark, and just start running around wrecking shit. And even though it's this writhing sea of insanity, with colors you can't describe and gibbering monsters and all kinds of other Lovecraftian nastiness, there are still planets there. Planets where gravity is reversed and blood rains from the sky and even MORE nastiness, to be sure, but planets nonetheless. There is STILL order and form in the Warp, despite what everyone says.
When it comes to the Warp, you really gotta throw out all the rules. Isn't that the whole point of Chaos? Maybe that's why Supreme Grandmaster or whoever can walk around without getting messed up. Or maybe it IS the Emperor, protecting a favored soul or something suitably inspirational. Regardless, the idea doesn't bother me that much, and I don't feel like it contradicts that fluff in a significant way.
What DOES horribly contradict the rest of the storyline, is the whole 'carved a name in the heart of a primarch' part. While I suppose it is possible that the greatest Grey Knight of all time, imbued with some kind of special-awesome Will of the Emperor-ness might be able to rival a Primarch, that character would be way too overpowered to be a part of the 40k tabletop game. Correct me if I'm wrong, but I've always operated under the assumption that the Primarchs would be way too overpowered to ever place in the game (even if GW wanted to)
"In the grim darkness of the far future, there is only war, an eternity of slaughter, and the laughter of thirsting gods. I'm telling you man, this is a really shitty time to be alive." -Primarch Stan Wolkowski, Sons of Stan