I access JSTOR, Science Direct and a dozen other databases via my university’s proxy. So, for instance, when I go to JSTOR, it is not to www.jstor.org, but to www.jstor.org.proxy.library.nd.edu. And when I access it that way, I can download pdfs of the articles, because my library subscribes. And when I visit the proxy page, I can direct Paperpile to add the reference, and it (usually) picks up the pdf as well.
But when I find results in google scholar, and click Add to Paperpile, it hardly ever picks up the pdf, since it attempts to get it from the public link. Instead, I have to click on the library link to my institution (which appears on the Google Scholar result page, because I had added the Library Link in my google scholar settings), then choose another link on the page that pops up, which takes me to the database via the proxy, and then either delete the current paperpile entry and get paperpile to make a new entry, or download the pdf and manually connect it to the Paperpile entry.
This is really less than optimal. I’d much prefer to be able to click the Add to Paperpile button in Google Scholar, and then trust Paperpile to remember that I access that particular database via a proxy. If I remember rightly, this is something that Zotero does, and it was a very convenient feature.