Convert to executable and compress methods override any stub you have created with their own stub which is responsible for extracting/executing self's content.
calling setStub() after convertingToExecutable doesn't help either. As far of php 5.3.6 (phar 2.0.1 ) if you want to have a phar archive accessible threw the web, you'll have to create your own
index.php which will include a nonexecutable phar and act as the bootstrap.