FranklyRe-roofing generally requires a permit
In San Diego, as across California, tearing off and replacing a roof covering is permitted work handled by your local building department — the City of San Diego for city addresses, the county or your own city for everywhere else. Small repairs below the local threshold usually are not. Your contractor should tell you which category your job falls into and why.
The permit buys you an inspection
A permitted re-roof gets inspected, which typically means someone other than the contractor looks at the deck and the finished assembly. That is a free second opinion on workmanship, and it is the main practical reason not to accept an offer to skip the permit.
Unpermitted work follows the house
Unpermitted roofing can surface during a future sale or an insurance claim, and the cost of resolving it lands on the owner, not the contractor who left years earlier. A discount for going without a permit is a discount you pay back later.
Confirm the permit is in the contractor's name
If a contractor asks you to pull an owner-builder permit for work they are performing, be cautious. It shifts responsibility to you. A licensed roofing contractor pulling work under their own licence is the normal arrangement.