I know if you
SetEnv MY_VAR 1
in your .htaccess file that you'll be able to
in your PHP script and/or program. If you can do it in .htacces, you can do it in your vhost configuration.
There's also php functions to set your php ini values.
I'm not sure about a way to populate $ENV, or is SetEnv will do it. It's worth investigating a var_dump($ENV) with the above.