A TC CD will try to load extensions and backup from any found drives. This lets you do things like carry one cd but have different data on a few computers.
Yes, this does mean that if you have an older TC install on the hard drive, booting CorePlus from CD will try to load things from the disk installation, which may prevent it from booting. IIRC you can add the "base norestore" bootcodes so it will only load things from the CD, letting you overwrite an older hd install.