Looks like E is excluded from variable_order setting running the built-in server. If you add the E to the variable_order setting, it works:
test.php
<?php
var_dump($_ENV['FOO']);
shell:
FOO=BAR php -d variables_order=EGPCS -S localhost:9090 /tmp/test.php
output:
string 'BAR' (length=3)
Tested on PHP 5.4.12