Your statement “While doing HOME PURCHASE one has to suffer a lot of problems, a lot of fees, unexpected charges, like application fees, process fees..” is absolutely untrue. All of the fees you refer to are covered by the lender in a NACA loan.
There are certain prepaids that are required such as inspection fees, the first year of insurance and at least two months reserves of mortgage payments in addition to the required payment shock savings. These determine the Minimum Required Funds (MRF) needed before closing. The Mortgage Consultant will be able to give you a good idea how much those will be as part of the counseling process.
It sounds like you may be confusing pre-paids like taxes and insurance with closing costs charged by the lender. Like Tim said, there are no closing costs, but you will have to pay your property taxes and homeowners insurance up front just like any other home purchase.
These amounts are prorated, so the estimate that you are given may differ from what you pay when you close. For example, if the property taxes on the home are $1000 and it is estimated that you will close on July 1, you will be responsible for half the year, or $500. If you close earlier than anticipated, you will be responsible for a little more.
It also could be the case that the property taxes are increased by the local government during your process, leading to higher than anticipated prepaid taxes on your part.