I think some of the folks below have answered your question pretty well â€“
I would add - having a decent amount of experience building through contractors, architects as well as on my own -is to be understand where in a project cost per sqf can go over the estimate. This could take place during the plumbing/drainage stage for example but most of the time it takes place during the â€œfinishing stagesâ€ - IE plaster, cabinets, fixtures, top flooring etc. â€“ being aware of this before you go into the project and to try and get some clarity around how this will be addressed (with your GC or arch.) before you start the project.
Lastly, make sure you speak with an insurance agent about what the replacement value is per sqf. as this too needs to be weighed into what type of project you may be willing to get yourself involved with - for example, if you build at $450.00 per sqf. and your insurance agent will only insure $350.00 per sqf (for new construction) you need to have a policy that covers the gap.
Good luck - and feel free to ask me any further questions.