This is an excellent topic. Planning is the most fundamental element to any successful project. Where I work, an aircraft manufacturer, order of process is essential for a proper 1:1 build. Of course, just like with scale models, there are mistakes and oversights that happen which must be fixed, so those repairs naturally are steps that are done out of sequence. But, those are anomalies. There are also certain steps that simply cannot be done out of order. For example, you cannot pressure test a fuselage or fuel tank before it is assembled. Don's questions above bring to light the reasons why nearly all aircraft modelers will finish (build, paint and weather) the cockpit before assembling the fuselage, and nearly all armor modelers will do the same with an AFV's interior before assembling the hull
The instructions that come with a model kit are nothing more than part placement guides. The desirable order of assembly may or may not resemble to sequence of assembly in the given instructions. I find it best to build as many sub-assemblies as possible before paint. In deciding what to include in pre-paint sub-assemblies, I consider how they will be painted (airbrush, hand brush, etc) and determine the difficulty and practicality of the work to be done. I also use this projection to determine whether a part may even be painted while still on the sprue
Also, exactly what work will be performed depends on the individual modeler's goals. That means the planning for the project will be unique to person or persons building the model. Though many modelers may follow similar basic steps, there will be many smaller tasks that will need a determination on order of construction. One must take all tasks to be performed into consideration in order to put together a solid work plan
This may sound like over-thinking, but it isn't. The importance is to visualize the build and plan logically. It's a pretty interesting task in and of itself, and it can lead to a more relaxing build, and more satisfying results