Deprecate url_preprint in favour of url_pdf (or a PDF file dropped into publication's folder) given there's now a dedicated "Preprint" pub. type. It would still be possible to link to a preprint by creating a custom link in the links option.
page_links.html (and possibly also btn_preprint from i18n)I would recommend to leave the url_preprint. Some people will be interested in having their preprint linked to a journal publication. It will allow people see the evolution of a paper, and it will also provide access to a PDF version of the paper, when the final published pdf version is only available through a paywall.
I agree with @santiago-schnell that it is convenient to have the preprint and the final published paper on the same document. The only reason I would change something is for clarity for the page viewer: maybe it would be more easily understood to have a "PDF (preprint)" button (rather than just "Preprint"). This said, some people may want to link to the arXiv/... page itself rather than the PDF (which would then be "Preprint", not PDF, but in my experience I would prefer have a special [custom] link saying "arXiv" in that case).
On BioRxiv preprints also get DOIs so if I have a project and I want my readers to be able to see various versions of the paper the "pre-print" is useful.
To be continued in #765
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I would recommend to leave the url_preprint. Some people will be interested in having their preprint linked to a journal publication. It will allow people see the evolution of a paper, and it will also provide access to a PDF version of the paper, when the final published pdf version is only available through a paywall.