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
0001-lisp-ox-latex.el-make-org-latex-prefer-user-labels-s.patch
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