When changing 'Load User Profile' to True, the profile of your Application Pool is loaded and is available for your application.
This can be used to isolate applications even further.
For example when this option is set to False ( the profile is not loaded ) and the application will use the c:\windows\temp folder as its temporary directory.
If one has other application pools, even they will use the same c:\windows\temp folder. If you set the option to load the user profile the temporary directory will be now change to use the profile’s temporary folder C:\Users\apppooluserid\AppData\Local\Temp.