I have a custodian who believes that if his church-run school adopts an ERISA-covered 403(B) plan, the school does not have to comply with the 3 optional ways to meet the contribution limits of 403(B)/415©. It seems to me that educational organization employees and church employees are entitled to the special elections of 415©(4), regardless of what the 403(B) document states and regardless of whether the church elects to be covered by ERISA and the Code.

Have I read this incorrectly?

The individual may be entitled to the higher limits, but that doesn't mean the church or the custodian has to accomodate them in the way they've set things up. It takes 2 to tango, and there's no law (that I know of) that requires a church or a custodian to allow employees to make the maximum possible contribution.