I finally decided my never to be finished (well, I would finish it, but my computer quits^^) Warhammer 40.000 Space Marine Battle Barge to be used within a picture! And as a huge Capital Ship as this one, never goes out alone I kit-bashed a Frigate kind of ship to give it company

The picture depicts a bettle within a planets atmosphere, between forces of the Imperium and an unseen enemy among the clouds. I really tried to show the size of that damn thing, but am not sure whether I succeeded.
Ships made in Google SketchUp, rendered in Kerkythea. Rest made in Photoshop.
The story goes on here:

Hope you like it!

Considering the madness that is 40k ships, shouldn't this pretty much set the atmosphere on fire? This deep in the atmosphere, since those explosions aren't over the horizon, so they must be only a few dozen kilometers away... they shouldn't be piddly little blasts of fire, but gigantic fireballs as the multi-gigaton warheads turn the atmosphere to plasma for dozens of kilometers around. Each engine burns with the fury of a small star, not just small trails of plasma, but huge, huge plumes of fire, far larger than the ship itself, pushing the vessel ahead at such speeds the sky explodes as it passes. It's such a tremendous cataclysm of energy that it really doesn't compare... these things consume more power than the entire modern earth just to accelerate. A battle between 40k ships involves throwing weapons at each other that make nukes look like water balloons...
Also, clouds can be the size of mountains. These things are bigger.
There's a reason 40k ships don't go in atmosphere.
Thanks man!
To be honest, I haven't given it much thought as of yet, I mean it's 40k. If it isn't over the top, it wouldn't be 40k. And such oversized vessels are a fine example of this!
But for the sake of argument, your points are completely valid. However you have to take into account, that this speculation is based on Earth as basis. Many planets are however terraformed, as such the composition and size as such mustn't be alike. As such this world could in fact have the volume of Saturn and an atmosphere that reaches up much higher than it does here, so the effects would be significantly different. Considering the strategical necessity, using their engines as weapons could prove valuable as well, but their output would be reduced in normal flight within an atmosphere, as the distance to cover are much smaller than in space. And if you decide to fight there, you would take the enemy position into consideration - a falling vessel with several kilometers in length can turn out to be much more of a weapon than a bomb
So, there's always a creative loophole for people like me, despite your reasonable and logical reason
The problem with lowering the engines is that those things are heavy, and just producing the force to counteract the force of gravity, let alone go anywhere, is going to be problematic. I suppose you could move around sub-orbitally, but... those big ships really aren't meant to fly in air. Think about trying to turn it!
Of course, there is indeed always a creative loophole... hey, there's that one that GW loves... the image is rendered to look pretty. Flaws in scientific/canon accuracy are because it's a painting 'in-universe', not a photograph.
Unfortunately, realistic space battles are tricky to depict, given the distances/speeds that tend to be involved. 40k ship to ship accuracy is kinda terribad, as tends to happen when you drag your starship cannons into place with manual labor, so you *might* be able to see the enemy ship without zooming in... but... yeah. Normally, you'll be fighting from such distances that an outside observer wouldn't see much - certainly not the beautiful battles of massive ships coming up alongside each other age-of-sail style and just broadsiding the crap out of each other...
Maintaining height may be achieved by anti-grav technology, who knows how that works? But you're right, they're definitively not meant to be within the atmo. But here I decided to go for style, rather than logic.
Concerning range: that is completely true. The distances are enormous! In my stories I try to depict this aspect, but in my paintings I decide (yet again) to go for style, rather than substance. Thanks again for your thoughtful comment! Always a joy to read and think about