Generally, yes. I can give limited insight for the US, and how claims have gone on my properties before... but maybe someone else can give better Canada-specific insight.
Usually whatever check you get from the insurance company is all you're going to get. That said, it sounds like your process is going a bit differently than I'm used to. My experiences have been that I pay out of pocket and then get reimbursed, or pay my deductible and let the insurance company handle the rest.
Where I have paid out of pocket for repairs myself (neighbor's tree fell on my apartment building's roof)... I submitted the full receipt to the insurance company... including tax... and was compensated in full. Obviously, minus the deductible.
Where I have dealt with making the insurance company handle it all... I have usually just stuck with the contractors arranged by the insurance agency.
In your case, it sounds like you're getting the insurance company to pay before the work is actually done? If I were you, I would recommend getting an all-inclusive quote back from the contractor and submitting that to the insurance company. My experience would say that they are not going to pay you more than once, and so I would make sure that you try to get everything included the first time.