I\'ve built from source php + php-fpm + nginx few times.
I\'m used to keep everything inside /usr/local
Hovewer php-fpm config file php-fp
You can compile php with the --with-config-file-path=PATH
compile-time option.
For your reference PHP Compile-Time Options
You can use a custom php.ini file using a .htaccess
with Apache adding le line
SetEnv PHPRC /location/todir/containing/phpinifile
To specify a custom php.ini with NginX check this link
As you pointed out you can use a CLI directive to choose a different php.ini
as well