On closer inspection, it looks like quite a lot of the javascript referenced in the pkgdown templates is not packaged, or has unmatched versions:
package, target, in-debian jquery, 3.3.1, 3.3.1 bootswatch, 3.3.7, 3.3.7 bootstrap, 3.3.7, 3.4.1 font-awesome, 5.7.1, 4.7.0 clipboard, 2.0.4, unpackaged headroom, 0.9.4, unpackaged docsearch, 2.6.1, unpackaged mark, 8.11.1, unpackaged mathjax, 2.7.5, 2.7.4 Given that pkgdown primarily advertises itself as generating static HTML documentation for web use, rather than traditional R man pages/vignettes, I suspect it isn't worth the time to try and reconstruct this HTML documentation. It appears to normally consist of an amalgamation of the README, changelog, man pages and vignettes into a single set of HTML pages. I think it's probably enough to provide each of those things separately as normal for an R package for those users who want to rely on offline documentation.