Hi @George Franz,
Since we don't know if you're experiencing any problems running the patch and how the redundant parts of the web.config file are affecting you, I'll provide you with some common ways to troubleshoot such issues:
1.Perhaps you have encountered error number 0x800700b7. You can refer to this article to fix it.
Reference: HRESULT code 0x800700b7
2.You can delete the extra parts of the web.config file and restart SharePoint in IIS. Retry to see if you are able to use SharePoint 2016 properly.
I hope this has been helpful. If it still doesn't solve your problem, we look forward to receiving further details about your issue. We will work together to help you solve your problem.
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