Section 6.6 of the Porter's Handbook discusses the use of USE_AUTOTOOLS, but makes no mention of the fact that they do nothing unless USES= autoreconf is also present. It seems like the general build procedure should insure this automatically, but it doesn't.
As it turns out, section 6.6 needs to be completely reworked, as the use of USE_AUTOTOOLS is no longer allowed.
Mmmm, everything talking of USE_AUTOTOOLS was removed in doc r51510.