I don't think modifications are going to work that way. It's more like an engineer can modify a specific hardpoint; i.e. giving you a blue laser that maybe increases thermal damage at the cost of heat. Or modifying your FSD to allow greater range at the cost of more fuel.
This is exactly what I've been wondering about since they announced "The Engineers". As far as I've heard, only the modules themselves will be modifiable, which I guess I understand, however, I also think it would be really fun to be able to change around compartments in a ship as well. I've also wondered though, if ships did become modifiable in the way the OP describes, and we can just make any compartment bigger or smaller at the expense of another compartment, wouldn't they really just become empty shells with no defining roles? Not sure really and I'm not sure what Frontier are planning, but I could see them, for the reasons I explained above only allowing modules to be altered.
All that being said, in keeping with the OP's original question, I can't wait to start playing "the engineers" and make many alterations to as many ships as possible, HOWEVER, there is one thing I am looking forward to doing more than anything else and that's making the fastest Cobra possible. I guess this will mean making as many modules as light as possible (if that's an option, which I really hope it is) While making the thrusters as beefy as possible. I'm also really looking forward to seeing what I can do with cooling, an ultra fast, super cool Cobra MkIII is my dream ship.