No, it does not matter who receives the allowance when a joint return is filed.
"A minister who receives a housing allowance may exclude the allowance from gross income to the extent it's used to pay expenses in providing a home. Generally, those expenses include rent, mortgage interest, utilities, and other expenses directly relating to providing a home. The amount excluded can't be more than reasonable compensation for the minister's services." Ref: IRS
This link Topic No. 417 Earnings for Clergy has information you may find helpful.
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