Did you have an earlier version of the SDK installed before? The installer doesn’t uninstall what existed previously, so the “CL” named version is probably just leftover from the older version. In the 3.3 SDK, we standardised the names of the utilities which included renaming PVRTexToolCL to PVRTexToolCLI. They’re the same tool, different name – CLI is the recent version.
As for the CPU thrashing, I’m afraid not at the moment. It uses all available cores to do the compression as fast as possible (because as you may have noticed, it’s an intensive algorithm!). We do have a feature request to add an option to limit the number of threads used, but it’s not implemented yet I’m afraid.