Hi,

I think that it is inconsistent that `org-latex-reference-command'
is a safe file local variable while `org-latex-prefer-user-labels' is
not (it makes no sense to set the first at file scope, while the second
is nil at global scope). Furthermore, `org-html-prefer-user-labels'
is also a safe file local variable.

The attached patch fixes this.

Regards -- Gerard