Now, how do I unlock the official "premium" modules (Kingmaker, Shadowguard, Witch's Wake)? They're also packaged in NWM format and don't show up in toolset or PRC updater...
You can't open them in the toolset. According to Bioware it is because of the security features that they put in. I am surprised that the PRC updater doesn't show them, but that might be for the same reason. There have been complaints about this on the Bioware forums, but so far there's no sign of it changing.
And you do have to rebuild the modules. It does take a lot of time, but the error messages are almost entirely harmless, in fact most of them are to do with resources that don't exist in the unmodified game. I've had the earlier version of the CEP installed on SoU and HotU with no problems for at least a year, so I don't think this version will be a problem. The PRC also works with these, though you have to use their fix with the original campaign.