After discussion with cjwatson in #ubuntu-devel, it looks like this is just a dpkg-specific packaging/build-rules issue; by default, packages will use dh_autoreconf, which will call autoreconf -f to force (re)creation of the configure file. The dpkg package has its own debian/rules call to autoreconf, however, and it doesn't pass -f.
This has been fixed (maybe unintentionally) upstream by commit c72f539b979a0c8647d2a6c62ee45565cd243b3d which moves the call to autoreconf into an 'autogen' file, but also more importantly changes the call from 'autoreconf -v -i' to 'autoreconf -f -i'.
After discussion with cjwatson in #ubuntu-devel, it looks like this is just a dpkg-specific packaging/ build-rules issue; by default, packages will use dh_autoreconf, which will call autoreconf -f to force (re)creation of the configure file. The dpkg package has its own debian/rules call to autoreconf, however, and it doesn't pass -f.
This has been fixed (maybe unintentionally) upstream by commit c72f539b979a0c8 647d2a6c62ee455 65cd243b3d which moves the call to autoreconf into an 'autogen' file, but also more importantly changes the call from 'autoreconf -v -i' to 'autoreconf -f -i'.