One thing that I'm not entirely clear on is the affect of the Warp on real space outside of areas that have overlap, like the Eye of Terror.

The Maw for example is a narrow channel through 2 Warpstorms. What is the physical space like though in those areas and the Maw itself? In real space is it turbulent to either side of the real space Maw, where the Warpstorms are? If you translate out of the Warp just before a Warpstorm hits (and the rift closes properly behind you let's say) what does the real space you just translated into look and act like? As I'm reading through the different RT books about the various places of interest I keep seeing varying effects of the Warp that seem to translate over. Just seeing if there is clarification.

A perfect example of Warp effects on real space is given in the Breaking Yards at SR-651 in Edge of the Abyss. Warpstorms cause huge gravity fluctuations. So I think I'm getting my answer.

Well, we now know thanks to BC that the spinward warpstorm above the maw is an area of warp/realspace overlap. As are the Haddex Anomally from DW, and the Rifts of Hecaton are strongly hinted as being the same as well. So I would say that any large, permanent warp storm has, at it's heart at least, an area of overlap between the materium and the imaterium.

We know from 40k lore that "smaller" warp storms that can cut off planets result in much higher birth rates for psykers and mutants, as well as a rise in cult activity and insanity.

I had assumed warp storms were just in the warp, but it increasingly appears that I was mistaken. I was most surprised to read in one of the books that you could see the Void Dancer's Roil from a location described in the book. Not how I was imagining it at all, and not sure I like it being like that. Oh well, I'm the GM, I can change it if I want.

I would assume that an active warp storm of any large magnitude is highly dangerous, and always avoided, when possible. No ship, regardless of its size or power, risks such a thing, unless they are sporting Chaos icons, and even Chaos is, well, chaotic. The storm, itself, would likely hurl incredible amounts of damage, both in the form of pure energy (and lots of it) and titanic gravity abnormalities (Hecaton is in reference to Hecatonchires, the 100-handed giants of Greek myth, and the pushing and pulling gravity fluxes will feel like that, for the short period you have a ship). More than likely, these would rip any ship to bits immediately, and kill anyone inside exposed. It is also possible that exposure to it would be like flying in the warp, so if you lowered your Geller Field, goodbye friend. In the warp, the warp is "calm" as your Navigators hopefully has you on a peaceful wave, but this is like a tsunami has slammed into you, with similar effect.

I know that in Lore of the Expanse, at the end of the last mission given, you MUST get off the Maiden World, or you WILL die. Anyone you leave there WILL die, and this is your incentive to try and save the Santarchs, if you allied with them. For ages, the planet was surrounded by a warp storm, but it was sitting in a lull spot, thanks to efforts by the Eldar. When you piss off the Farseer (Serennon), he calls the full power of the storm back down upon the planet, eliminating the calm zone around the planet. You are given several ways to escape, but it is strongly implied that you must, or you will be destroyed. This is also why no one can just go back later, and keep looting the planet, or take up ownership; the full-bore warp storm makes the planet worthless, and lethal. One could probably compare it to being strapped into a chair, and having a Navigator look at you, nose to nose, and slowly open his third eye. The Warp will reach out and obliterate you. The warp storm might be looked at as realspace opening its warp eye.

I figure one of the strongest weapons in Battlefleet Gothic is the Warp Cannons on an Awakened Blackstone Fortress (right up there with Abaddon's Planet Killer and the volleys possible from either Iyanden Craftworld or a Ramilles-class Starport). The warp cannon can obliterate most anything in one hit, and the warp storm is a much higher magnitude that.

So, anyone, or anything caught is probably written off as a bad pilot, or a very unfortunate one, at least. I suppose, with full void shields and Geller Fields active, it might be a very bumpy ride, albeit survivable, but I'd lean more toward a bad ending for the party.