the ebuild for php has --with-apxs hardcoded in the ./configure portion of the build. this should be optional, as many will desire the option of installing the binary executable (/usr/local/bin/php). one suggestion is to have the ebuild build both the apache module and the php executable. as far as i know, this requires two ./configure&&make&&make install runs.
This is true. The new php-dev/ directory I am working on will include a php_mod and php package. it may be possible to use the new USE format being proposed to pass an option to emerge to compile for commandline and mod support...