Thank you for your patience. I have successfully tested this pdftk installer and binary on OS X 10.11, El Capitan:
https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/pdftk_server-2.02-mac_osx-10.11-setup.pkg
I will update our PDF Labs site soon to reflect this update.
If you already have pdftk installed from the old installer, this should install right on top of it without a problem — it shouldn’t be necessary to remove the old pdftk before installing this one.
Note that this installer/binary has not yet been tested on older versions of OS X.
Please let me know how this works for you.
I want to thank Aaron for opening this thread and for bringing helpful attention to the problem we were having with the build tools. I also want to thank the MacPorts team for their professional and timely work!