Graham,
I can't treated heads textures the same as pilosities because ... they are textures!

So, a quick fix would be to rename head texture files, in order to adopte the same naming convention as clothes textures. But then, you fall into a design problem: each texture set will adopt an arbitrary head texture.
I think prepare separated NPC into separated folders is really the best choice. It allows you to mix the texture parts of different sets, and to choose any head texture for any NPC.
Also, use the SetSkinName extension (
http://www.garagegames.com/index.php?sec=mg&mod=resource&page=view&qid=7154) can be a good choice.
So, no, it's not a bug, and I asked myself this question when I designed the pack.
So, if diversity is not a priority, then, rename head texture files. But if NPC diversity is an important part of your project, prefere to use the pack as describe in the documentation.
Christophe