Are you saying for the first one, a portion is recovered each year until fully recovered? Yes. Pro rata until the tax free portion is completely recovered. Plan administrators do not manage this, taxpayers have to.
For the clergy question, is the housing allowance excludable from SE tax? No. Income tax
only. http://www.irs.gov/publications/p517/ar02.html is the link to IRS Pub 517.
From that Pub.:
"Exclusion of Rental Allowance and Fair Rental Value of a Parsonage
Ordained, commissioned, or licensed ministers of the gospel may be able to exclude from income tax the rental allowance or fair rental value of a parsonage that is provided to them as pay for their services. Services include:
Ministerial services, discussed earlier,
Administrative duties and teaching at theological seminaries, and
The ordinary duties of a minister performed as an employee of the United States (other than as a chaplain in the Armed Forces), a state, possession, political subdivision, or the District of Columbia.
This exclusion applies only for income tax purposes. It does not apply for SE tax purposes, as discussed earlier under Amounts included in gross income under Self-Employment Tax: Figuring Net Earnings. "