The closest thing to designing and building an organization is the designing and building a house.
You can build a house with pre-existing replicable architectural plans. See those metastatic new towns or Clone-Villes where every house looks like the neighbours. It’s a cost effective building, predictable and with little differentiation. Many companies are built like this. There is a template of what a pharma company or a bus company looks like. The only difference with them are the products or the routes. You go inside the door and you can predict the departments that you will see. Their organizational charts are the same with different names in the boxes.
You can build one from scratch but borrowing from other models, a pick and mix architecture that may end up sublime or ridiculous. This is the building of a bit of A and a bit of B, plus perhaps something original.
You can build the house from zero, with 100% of the design for the purposes of the family. You start with a plot, a view and money in the bank. The rest is commentary. A pure start up follows that. As soon as there is a bit of growth though, it may start looking like a bigger cousin. Or it may not.
You have a house already, or sort of one, and make it better, bigger, more energy efficient, with an extension for the kids, new garden and, not to forget, that Jacuzzi in the corner. And variations. Most organizational designs start from a pre-existing structure, something already in place. Vast empires have been created from old templates. Just to remind ourselves that 3M stands for Minnesota Mining, and Manufacturing and I have not seen much of their mining recently.
You can pretend you built a new house, explain to everybody that it is a new house, but it is in fact a massive redecoration of the old one.
I will stop here with analogies. There are plenty more.
My rule number one as organization architect is that you should not start with a picture or a drawing of the house, as much as this is very attractive and the desire of the ones who will pay the bills for the building. Our building blocks at The Chalfont Project  are three different sets applied to old and new, redecorating or greenfield building:
- An Enabling Design. A ‘structure’ so that the activities of the organization can be facilitated, enhanced, not impaired. Regardless of the ‘final look’. Many organizational structures are clearly not enabling. We know that a very hierarchical design does not foster innovation. You can’t have an army formed by totally self-managed units either.
- An Operating System. A set of rules and (social) algorithms that make the structure work and that can cater for many ‘activities’. Decision making rights sit here, for example. Designing an operating system is more than designing processes. Anybody can design a process on the back of an envelope.
- A Mobilizing Platform: a way to mobilize and engage people to get things done. The mobilizing platform is largely ideological (ideo-logical, that is) but has to be workable in (2) a particular operating system and (1) a particular design. Here it sits The Viral Change™ Mobilizing Platform. 
A typical Organizational Development error is to assume that (1), structure/design, dictates de facto the operating system you (will) have or the way people will be engaged and mobilized. It doesn’t. You need the three legs above completely in sync. Also, touch one of them, you touch the other two even if you don’t realise it. The Fundamental Design Error is attributing to an organizational chart (structure) magical powers to ‘produce’ an operating system and a mobilizing platform.
People has asked me to write about the minimal ‘principles’ of organizational architecture. Here they are in a slim version, enough I hope to reflect and trigger some ‘so what thinking’.