>>> Unpacking source...
>>> Unpacking firefox-1.5-source.tar.bz2 to /var/tmp/portage/mozilla-firefox-1.5-r7/work
* Applying firefox-1.1-nss-system-nspr.patch ... [ ok ]
* Applying firefox-1.5-with-system-nss.patch ... [ ok ]
* Applying firefox-1.5-visibility-check.patch ... [ ok ]
* Applying firefox-1.5-visibility-fix.patch ... [ ok ]
* Applying mozilla-hppa.patch ... [ ok ]
* Applying mozilla-firefox-1.1a2-ia64.patch ... [ ok ]
* Applying mozilla-jslibmath-alpha.patch ... [ ok ]
* Applying firefox-gentoo-pkgconfig.patch ... [ ok ]
* Applying firefox-nopangoxft.patch ... [ ok ]
* Applying firefox-1.1-uriloader.patch ... [ ok ]
* Applying embed-typeaheadfind-1.patch ... [ ok ]
* Applying mozilla-firefox-1.5-gtk.patch ... [ ok ]
* Applying firefox-1.5-safetooltip.patch ... [ ok ]
* Applying mozilla-rpath-1.patch ... [ ok ]
* Applying mozilla-1.7.10-nsplugins-v2.patch ... [ ok ]
* Applying mozilla-firefox-1.5-history.patch ... [ ok ]
* Applying mozilla-firefox-1.5-mork.patch ... [ ok ]
* Running eautoreconf in '/var/tmp/portage/mozilla-firefox-1.5-r7/work/mozilla' ... [ ok ]
>>> Source unpacked...
That is with portage 2.1_pre3-r1

as you can see it is already running eautoreconf ${S} as it should be.