Yes, POPFile works with SPA/AUTH. Please read the manual for details. Here is a Howto for Eudora users.
Do we handle this any better now? Looks like we do: Quick Start Guide: Using POPFile with Secure Password Authentication
This page needs updating then.
Should you find anything in the documentation that is incomplete, unclear, outdated or just plain wrong, please let us know and leave a note in the Documentation Forum.