Individual contact type select is missing in custom field group setting
I now understand why the individual subtype select was not appearing. It was simply because one of the fields was being used. The As soon as you fill in one of the custom fields of a field group then the option to change type and sub-type is removed. 

I was misled by a cosmetic bug that it does not display the sub-type "any" when beside the default "individual" there were added subtypes afterwards. I will try to reproduce and report this, to prevent that others are misled by this.