>>You can specify the .Net version in the AppPool Basic settings.....
>
>Yes, but without those settings, what drives the decision to know what framework would be used?

Oh, I see what you mean. See:
http://blogs.msdn.com/b/webdev/archive/2012/11/19/all-about-httpruntime-targetframework.aspx

Snip:" If the targetFramework attribute is not present, we assume a default value of "4.0" and run the application in quirks mode."
So, seems to me that the only way to ensure the 'latest' version is used is to specify the targetFramework in the config file.