Where in the Code you have set out does it say the IRS differentiates between incorporated and unincorporated churches? There is no difference. The IRS looks at the organization called "church" without distinguishing corporation from unincorporation. Look at form 1023 the Application for 501 (c)(3) recognition.
I have explained that before in my posts #26 and #34.
508 of the IRS code allows an automatic exception for churches. It doesn't say "exemption," it says, "...churches have a mandatory exception." The exception is from filing a Form 1023 to make application for not for profit status and from filing the annual Form 990. (note a church may voluntarily file these forms but it is not required.)
Incorporated churches because the IRS sees them as tax exempt corporations are not eligible for this exemption. They must file a Form 1023 and the annual Form 990.
The IRS does indeed differentiate between the two.