Copyright of copies of public domain artworks is odd: the original artwork is not under copyright, but a photo (and possibly a scan?) of the artwork can be. The US legal theory (I don't know about elsewhere) is that a photo of a public domain artwork can itself be an artistic creation, deserving of separate protection.
For example, the photographer might have made an artistic choice to use a diffuse white light without glare, to have the entire frame in focus, and to crop the photo at the edge of the artwork. It is commonly thought that a mechanistic scan fails to meet this ridiculously low threshold of creativity, but this defense has not been well tested in the courts.
So in the absence of a contractual agreement to the contrary, if you make a copy directly from the original, you are likely legal. But if you made a reproduction from a reproduction that could be considered itself an artistic work, you could be infringing on the copyright of that reproduction.
I don't know what the rule would be for making a copy of an authorized "slavish" physical reproduction, but given the low bar for copyright, I'd guess it would still be considered infringement? Anyway, here's an overview of the legal situation in the US: http://blogs.library.duke.edu/scholcomm/2013/06/14/museums-c...
Here's a link to someone who went ahead and created his own physical version from the published scans, printed on a color laser printer, then 'aged' by dunking them in coffee: http://scienceblogs.de/klausis-krypto-kolumne/2016/08/27/pub...
Here's a link with a little bit more detail about the arrangement between the publisher and the library: http://www.thelocal.es/20160821/tiny-spanish-publisher-clone...
Finally here's the page about the Manuscript on the publisher's website, which might have more information if you read Spanish: http://voynich.siloe.es/manuscrito/