Having work done to your home without going through the local building department permit process saves you permit fees and the hassle of meeting city inspectors to approve and sign off on work. If you make changes in your plans along the way, this can involve further design review. But, it can cost you money if you end up with a remodeled home that won't appraise for the price buyers are willing to pay when it's discovered that the work was done illegally.
Some planning departments won't issue a new permit if there are any outstanding permits that did not receive final approval from the city inspector. Buyers, who discover this after they've closed on the house, will have to make the corrections before they can move forward with their plans.