And are any of those things not programmatically available (.Net) from Microsoft.Web.Administration?
When you recycle an application, the worker processes (w3wp.exe) are shut down and new ones started.
When you perform an IIS Reset you restart the following Windows services:
IIS Admin Service
Windows Process Activation
World Wide Web Publishing
The worker processes depend on these services, so naturally ALL worker processes (not just the ones pertaining to the application you would like to recycle) are shut down, and can not be started until the WWW Publishing is ready to process requests again.