The 3% statement was simply a rough estimate.
Appraisals are something done to close the loan, and its often paid at settlement, so its a closing cost.
It may be paid in advance of closing though, then it would not be a cost paid at closing, but its still a cost to close the loan.
If someone asked me to do their loan, and asked for a quick guesstimate on their closing costs, I'd say 3% of the sales price too, but in my head that would not include the home inspection fee.
Bottom line is, get a GFE ASAP.