Insurance adjusters don't set the price. They simply scope the damage to the property and measure the amount of roofing and other collateral damage. They use different pricing programs to figure the cost to repair or replace the damaged property. Its possible that they don't see all the damage or measure the roof properly but In most cases, they are able to get right on or close enough that there wouldn't be to large of a gap between their estimate and the contractors estimate. If they do miss something or don't measure properly, you and your contractor can file a supplement and the insurance company will pay the difference if there is documentation showing where the missed or unseen repairs are. Depending on the amount of loss or the cost of the repairs sometimes dictates how the claim is paid out. Here is how it typically goes................... ( I'm going to use hypothetical numbers below)
Total amount of claim +10,000.00
less depreciation - 2,000.00 (depending on your policy this money may be recoverable if all the work is completed and it will be paid at the end)
less deductible - 2,000.00 (this is your responsibility. plenty of contractors will cover this for you but you will definitely get a **** job if you choose one of these guys because they will cut every single corner to make up their profit they lost by "covering your deductible")
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ACV (actual cash value) = 6,000.00 - This is usually the first of 2 checks you will receive. After the work is completed, you would file for the recoverable depreciation (2,000.00 from above) and they will send out your final check.
To sum up - You should be able to get your entire roof replaced for no more than your deductible. The exception to this rule is if you decide to upgrade your roof then you would also be responsible for that additional cost which is above and beyond the claim amount.
If for any reason, the contractors numbers and the insurance companies numbers don't match, than someone either mis-measured or one of the parties pricing is off. Either way, the insurance companies number one goal is to get your claim resolved and paid for as fast as possible. Feel free to ask any questions. Hopefully this was helpful.