I've successfully added support for QuArK's enhanced texture positioning MAP format, so that means that my version of QBSP3 matches Armin's in terms of functionality, while incorporating most of GDW's enhancements. Yay!
Lots more stuff to do, though. In particular, I want to remove the way-to-frequent appearance of printf in the code to do debugging/error reporting and centralise it into some utility functions (probably in cmdlib.c -- this is the way Armin's QBSP3 does it, by the way). And that's on top of fixing the origin-brush-displacing-textures problem.
Get the Windows build from my downloads directory.
Update: Uploaded new Win32 build with stripped binaries (i.e. download is now a tenth of the size).