I see this was posted long years back. The .net instrumentation have been improvsed over the years. there is no need to mess with the app pool monitoring unless needed.
in the "resticted instrumenation" portion of the "introscopeAgent.profile", only managed applicaiton / applications pool for IIS 6.0 and above are instrumented automatically. Eveeything else reamins disabled until one enables it. In 9.5 it looks as below -
# To restrict instrumentation to ASP.NET applications only, set the property
# introscope.agent.dotnet.monitorApplications to w3wp.exe for IIS 6.0 or later
# and aspnet_wp.exe for IIS 5. Add additional executable names to the list
# to instrument them. Full pathnames with single backslashes are also
# acceptable. For example,
introscope.agent.dotnet.monitorApplications=w3wp.exe,aspnet_wp.exe ----> only this is enabled for my apps
# Uncomment the following property and specify IIS application pools to be instrumented.
# Application pool names must be in quotes. Use "NULL" to specify applications not running in any application pool.