No, there are some differences like:
- rootkit scanning enabled by default in CCE, not in CIS,
- scanning for MBR infections in CCE not in CIS,
- scanning for abnormal system settings in CCE ,not in CIS,
- more aggressive disk access methods in CCE, not in CIS,
- scanning for "bad certificate" files in CCE, not in CIS,
- scanning for infected partitions in CCE, not in CIS,
These are all I am able to think about now.
I think CIS scans for rootkits by default. The option to enable rootkit scan is an advanced rootkit scan i.e indepth rootkit scan. This can give FP's so the option is not enabled by default.