It may be unlikely that two pagination formats will have a document element root, but certainly possible. It is highly likely that a generic xml handling solution will have to deal with many different formats which have root as the document element.
XSL-FO is not a compelling argument for namespaces, given that XSL-FO documents are generally fed directly into programs expecting XSL-FO, with no need for disambiguation.
One could imagine two different markup languages both having a root element of <fo:root>, and a formatter that supported both markup languages, and yet such a thing does not exist.
Namespaces on the other hand do exist, apparently to solve non-existent problems, while causing real problems of their own.