In the file authentication-services-context.xml the bean 'homeFolderManager' decides which HomeFolderProvider to use.
By default this is 'personalHomeFolderProvider', which creates personal homes under Company Home. To have them created under User Homes instead, change the 'defaultProvider' property of the homeFolderManager bean to use 'userHomesHomeFolderProvider' instead.
If you wish to avoid editing this Alfresco file directly, override the homeFolderManager bean entirely in a context file in the extension folder (I assume you are already using the ntlm-authentication-context.xml file there, so you might want to use that one).
Regards,