To clarify, comments never affect running code in PHP, ever.
What's often done however is that tools like ORMs, or web frameworks offer a 'compile' step that parses these annotations (just like it's common in Java) and dumps a PHP file that maps things in the annotations into actual PHP code.
For example, you can use it in Symfony to wire routes to handling functions in controller classes; or in Doctrine to help the mapper wire Entity classes to database tables.
If you don't like the idea of preprocessing annotations, you can totally not use them and configure everything using external YAML/XML files.