.NET ThreadPool and Configuration-Collection of common programming errors
As you have noticed you cannot change the ThreadPool configuration from a global machine configuration file (machine.config) or an application level configuration file (app.config or web.config for ASP.NET apps).
As explained here: Configuring Threadpool Max Threads via app.config? you can do it by code, eventually reading the settings from a confg file manually.
This implies that changes done in this way at runtime are limited to your application, surely do not span across other running processes on same server or machine.