The addon linked from the pdf.js issue is now non-existent.

The current workaround is to choose Firefox itself as the "Open with" application. It opens correctly but through this process the original URL is lost because it's being opened from a (temporary) file.

It might even make sense to have an additional "Preview in Firefox" in the download dialog for this reason as it is applicable to all file types Firefox itself can open (e.g. images), not just PDFs. It's worth solving this in general, not specifically in regard to pdf.js. Also, it must be noted that "Preview in Firefox" is already an existing choice in Preferences -> Applications, along choosing external program and saving into downloads, so it makes perfect sense for the same preview option to also exist in the dialog (which corresponds to "Always ask").