The final dimensions is one of the deliverables of your final design. You need to understand the magnitude of your design - one thing a friend of mine does in job interviews with young engineers is gives them an engineering drawing and asks "how big is this item? Can I hold it in the palm of my hand?" He is a machine designer and so deals with small components that need to all be designed to work together in a very small space.
I however design process piping so I know that my design will take up a lot of space before I start - I may have to negotiate for more space. If it is a new plant then I have more options but if I am designing piping to fit into an existing plant I have much less options. I have to think about the space required not only for my design but for the other disciplines coming after me. For example, How big will the pipe supports be? where can we fit them? where can we fit in the new pipe support footings? What about the access platforms? Do we need to fit in flow measuring devices and do they need certain straight lengths of pipe upstream and downstream.
In this piping example you can see the final dimensions are an integral part of the design and most dimensions have been selected for a reason. The design will develop overtime and an initial concept will progress into a detailed design as more of the parts of the design become certain. EG the final pump models may have been selected and the size of the pumps may be different than the pumps used for the concept design, hence the nozzle loads on the piping may be lower hence the piping needs to be modified.
Reading your post I suspect you are more into machinery design. However the design process would be the same - you may have a concept design with some gears and bearings and things but then you may find in the detailed design that you need to change the bearings and need more space. Over a period of time your design will develop and the dimensions will come out as part of the design.
In many ways, broken down to its basic format design is making sure the dimensions are correct and everything fits together to work in the way it was intended, be it a piping system or a machine.