Building a house in sections over time
Assuming you have a floor plan that you like, there are 4 main issues: 1) Building Codes, 2) Planning Department, 3) CC&amp;R’s, 4) utilities. 

1) The Building Code requires certain building requirements that may not be apparent with a small house, but is required in a larger building, (i.e.: shear walls, larger footings for brick or stone walls, setback requirements, etc.) 

2) The Planning Department has requirements such as maximum lot coverage, setback requirements, etc. 

3) CC&amp;R’s, if any, have specific requirements such as minimum size house (mini-mansion sub-division), maximum height restrictions, etc. CC&amp;R’s are included in your “paperwork “ when you purchased the property. I’d re-visit your documents and make sure you understand terms like, “sight lines”, “natural materials”, etc. 

4) utilities are difficult to re-do half way through a project. If you are on a septic tank and drainfield, your soil may only allow a two bedroom house, etc.

Therefore, I’d recommend you provide plans and specifications for the “final” design, not for the initial construction phase. Btw, codes and planning issues change from time to time. So, getting the entire project approved now will negate any changes that come along in the future. (However, most Building Permits have a time limit. I’d verify with your local jurisdiction.)