Weapons, engines and mods, Oh my!

[Suicide Junkie]

That's cause the shuttle is a really small ship. That's where the engineering difficulty lies.

Check out the shuttle on launch... its a little teeny bridge, a cargo bay to make it useful, and the rest is all engines.

There is no reason why you can't have a ship that is a little bridge/lifesupport/crewquarters combo, sitting on top of a huge pile of engines.

Just look at any Earthly launch vehicle these days. 95% engines.

Even with a low-surface area ship, you can put the fuel tanks in the middle and have lots of tubes running to the nozzles at the back