By putting the Reuse project and the GNU project against each other I tried to favor a small targeted project compared to a large, seemingly all-encompassing effort. But as you showed me, even GNU has its points of focus.
With regards to funding, there might be other organizations willing to sponsor an effort, as long as the goal is clear. So that is where to begin.
In regards to the PDF issue, it makes sense to first get an idea of the scope of the problem. Like I mentioned, I heard some reports about this issue, but am not aware of the current problems on this topic. Collecting theses reports can help to scope the issue: what organizations are not using open standards, what proprietary extension are we talking about, and what use-cases does it relate to? Then we could move forward by requesting the organizations to adopt open standards, by suing them into compliance, or by developing software that provides a workaround.
The pdfreaders.org website currently lacks information on typically used extensions. Also there is no way to file a complaint on a specific case that could help paint a better picture of the current situation.
Kind regards, Nico