One of the things I hate about modern space-ship building games is that they always produce the same kinds of visual profiles: boxy, utilitarian. 45-degree angles are considered the height of fashion. People can go out of their way to build interesting ships, but if they do, it is at the price of lower efficiency: more weight, more vulnerabilities, etc.
Now, I don't actually hate boxy ships. I just don't want every ship to be boxy.
Gravity Grain features a similar kind of construction system. If I don't go out of my way to make another kind of layout preferable, Gravity Grain will have boxy ships.
The major mechanic Gravity Grain will use is "exclusion zones" - (usually) spherical zones of danger around specific modules. For example, a fusion reactor might have a 200m heat exclusion zone, while an inertialess drive might have a 300m "gravity wobble" exclusion zone. In theory I could model propagation and stuff, but it's easier to both model and understand these things as spheres in space, regardless of how full or empty that space is.
As you enter the heat exclusion zone, your suit would have to work overtime to keep you cool - your time here is limited to your battery life. Similarly, there are many kinds of things that can't function while in an exclusion zone. A bed can't be slept in. An IR transceiver can't broadcast. A telescope can't focus.
More critically, if any two exclusion zones overlap, that area is destructive. If you have two reactors close to each other, or a reactor and an inertialess drive, the place where they overlap will quickly cause damage to anything in that area, whether it's a tile or a person. You can easily rip your own ship apart, and you probably will do exactly that at first.
Obviously this means you have to spread your ships out. That'll be the first thing people learn when building a ship, and I imagine we'll see a lot of long, cylindrical ships from newbies.
But there are a lot of clever tricks hiding under the surface, if you want better performance. Use nacelles: the space between them might have overlapping exclusion zones, but it's just empty space, so it's fine. Use ship modes: balance modules that produce exclusion zones so they either scale back as another one scales up, or turn on and off such that no two ever overlap. And, of course, the ever-popular mechanical extensions - swing things far from the ship to turn them on...
You can even creatively use exclusion zones as shields or weapons, if you're clever. Fire an "inertialess missile" at an enemy, and wherever its field overlaps with an enemy's own internal fields, the enemy takes damage. Doesn't even have to hit - actually, it'd be most effective if it was fired at great speed, then decelerated to a relative stop and just sat near an enemy. Gatling turrets are your best friend, I guess.
All of these reasons lend themselves to spread-out ships. In addition, mass is not as big a concern in this game - structural elements are very, very light, so wasting space on them doesn't really affect your performance characteristics. Of course, those kinds of lightweight elements are also very, very easy to rip apart...
And there are reasons to want a dense ship. First off, a dense ship is easier to land. Also, FTL speeds are based on bounding boxes, so dense ships are faster at warp, if only modestly. Lastly, dense ships tend to have their critical systems in the center, well-protected against meteorite impacts or weapons fire, and are very hard to physically sunder, unlike ships that are mostly long, frail connections. Obviously, a dense warship is also much easier to properly armor, as you need much less armor.
The warp speed thing alone should lead to some fun "fold-out" designs, where the ship is sleek in warp mode, then drops into realspace and extends various kinds of projections, wings, and so on, unfolding for better exclusion-zone performance.