It turns out the answer to my question was much simpler than I expected
When deploying to the root folder of an application using MSDeployPublish using MSBuild, by default, the extra subfolders located in the file system of the target IIS server are deleted.
To avoid this, I simply moved the contents of my DotNet folder to a completely different place under C: \ InetPub, but retained my original virtual folder / application structure under IIS Mgr. Sure!
Now I can publish anywhere as much as I want, and no one will try to delete another, because it is no longer a subfolder of the other's file system.
If anything - this emphasizes how primitive our previous folder structure is, and what kind of doofus I am for not understanding.
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