Your environment does not have support for treating PDFs as images.
PHP was not compiled with the Imagick extension. While your server may have the ImageMagick binaries installed, along with the appropriate GhostScript extension, which was needed in vBulletin, vBulletin had provided command-line access to the binaries, while XenForo requires the presence of the Imagick PHP extension.
In your environment, it would be necessary to download the PDF in order to view it. The link in the wiki page sends the user to the correct download page for the PDF.
The only issue I notice here is that the generic file icon is not showing when FILE has been used in 'thumbnail' mode and the file cannot have thumbnails. I have fixed this in the next release. Everything else you describe is working as designed, and by the way, it's exactly how the FILE BB-Code (then IMAGE) worked in VW3, so it is in no way a step back or a regression. Your gripe is with the conversion of ATTACH to FILE in VW4, which gives all wiki attachments a separate description and download page, has been litigated ad nauseum elsewhere.
Marking this as Working as Designed.