I\'m trying to compile a new instance of PHP (5.4.0) from the source code and want to keep compatibility with the one (PHP 5.3.6-13ubuntu3.6) already installed from the dist
According to this bug report, the Configure Command output was intentionally suppressed from Ubuntu & Debian PHP builds.
Then recommend installing the source package via apt-get source php5:
If you want to see how PHP is built in Ubuntu,
apt-get source php5, and peruse debian/rules, the ./configure output in phpinfo() is, as the changelog for the patch states, entirely misleading and not terribly informative.