We often think about the OSI model, Three-Tier architecture, Capability Maturity Model and your favorite mantra:
Make it work. Make it right. Make it fast.
A layer is just that, a conceptual model to aid us in breaking down the complexity of a process. Once we get to the implementation stage, the layers will guide us dealing with trade-offs brought about by our conceptual model.
In the end, the machine does not care. After you deployed the software, to a machine everything is just bits of 1 and 0 (there are no layers).
The implementation process is not sequential. It can be iterative. It is a matter of knowing the trade-offs.
The conceptual layers only serve as tools of our thought processes.