If a congregation provides an in lieu of FICA benefit to ministers, it should be based on salary + housing. That's because ministers pay SECA (the self-employed* person's version of FICA) based on their entire salary and housing.
Our Ministerial Compensation 101 article can help with this and other compensation questions for ministers.
*Remember that ministers are considered self-employed for social security/Medicare, but an employee for all other purposes.