The likely issue with these is you are assuming that the internal UI does a full audit and will tell you that you have an available set based on a full verification. MAME only validates roms at runtime and will inform you what you are missing. For quick determination of if you have a machine or not, it will look for either a compressed folder (.zip/.7z) or a folder with the shortname of the machine in question.
So, in each of the instances you list, the most likely scenario is that roms are taken in whole or part from the parent but the CHD is likely unique for that version and not taken from the parent set. MAME will not detect you have something via its internal scan unless you have a compressed folder or regular folder with the same shortname. So, the answer that "you are missing CHDs" is a completely valid observation.