You definitely need to be careful about using relative paths in after the shutdown function has been called, but the current working directory doesn't (necessarily) get changed to the web server's ServerRoot - I've tested on two different servers and they both have their CWD changed to '/' (which isn't the ServerRoot).
This demonstrates the behaviour:
<?php
function echocwd() { echo 'cwd: ', getcwd(), "\n"; }
register_shutdown_function('echocwd');
echocwd() and exit;
?>
Outputs:
cwd: /path/to/my/site/docroot/test
cwd: /
NB: CLI scripts are unaffected, and keep their CWD as the directory the script was called from.
