That's exactly the problem.No engineering space on a modern ship looks that 'neat'.Any plausible engineering bay on a 762 meter long starship capable of FTL speed is gonna need some basic elements,like coolant tanks,water tanks,computer rooms(or farms),batteries,plasma conduits,and the warp reactors themselves.Plus you have the environmental systems like oxygen generators,HVAC systems,water supply,heating and cooling elements.All that stuff is gonna need to be connected to the other 'stuff' somehow-the coolant has to get to the core,the antimatter has to get to the reaction chamber,the power has to be transferred from the chamber indirectly to the devices that need the energy,the Bussards I'd imagine generate heat and require cooling -all the above need to be tied in,and you do that using pipes,joints,and conduits.Seeing as how you'd need a LOT of energy to run the Enterprise,in turn you need a lot of everything else to make the ship liveable,and to keep it from blowing itself up via overheating.
This desire for a 'clean' engineering bay doesn't work-its like opening a car's hood and wanting to see just the motor,without wanting wiring or coolant lines to exist.