This article gives a better 'friendly' description of what the rules do:
Prevent hijacking of .EXE and other executable extensions
This rule protects the .EXE and other keys under HKEY_CLASSES_ROOT. Some viruses alter
these keys to ensure that the virus is run when any other executable runs. Enabling this rule will prevent
spyware and malware from modifying important operating system and executable files.
Included processes: all
Excluded processes: installers
You can deduce from the explanation it does not cover the IFEO keys.
Which exes and areas of registry are protected?
How does it stop viruses to alter files?
I guess I just want to verify that some changes are taking place on the system.
I am not permitted to post specifics for you (requires an NDA).
I can describe for you that it protects hijacking the execution of .EXE files, .BAT, and .COM files.