I’m not sure if I understand correctly what the problem is. You say that PDF files downloaded in Safari with the Adobe PDF Viewer are unreadable by DT, but those downloaded with the Schubert plug-in work? That should not make any difference, as the PDF files come from the net, not from the plug-in.
No. The problem is with viewing PDFs from within DT when browsing the internet.
That is, when I’m browsing the internet with DT, sometimes I come across PDF files. If I have the Schubert plug-in in my Internet Plug-Ins folder, I can view them (not download them) within DT. However, if I have the Acrobat Reader plug-in, I cannot view them: DT just loads a blank page.
I wouldn’t be surprised if this was a problem with the Adobe plug-in, not with DT. Still, it would be nice to be able to choose which one to use.