Yep, that's what I was thinking too. Even a simpler cross-compiler toolchain without any kind of cpu transparency would be useful for most native applications -- save for ports of already existing GNU packages, mostly have no need of overly long "configure"s requiring complete sbox-like environment (and thus can work in a cross-compile env that can't run compiled binaries). Then a simpler buildpackage tool (written in standard portable C) could do the job of creating the .deb file; it just needs to tar the appropriate files.
(See the iPhone GNU toolchain for examples)

Of course the debugging/emulation issue is still there, and sbox should be still there in case the need for anything more complex arises.