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@AQUI wrote:

my active minister client brought a 1099 R stating the financial company told him he can use the total amount withdrawn as housing allowance to purchase a house. 

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Housing allowance has nothing to do with this.  Also, not for the total amount, only up to the lifetime limit of $10,000 for first-time homebuyers.  And there are conditions.  Normal taxation rules for distributions still apply, just that early distribution penalty would not be assessed.

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I know he can use part of the withdrawn amount as down payment, and to cover all related expenses to maintain the house. 

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This is not correct.  The exception is only for qualified acquisition costs.  Expenses for maintaining the house would not qualify.