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
