No, VSC has no understanding of PHP's auto_prepend_file configurations. No IDE will, actually. Additionally, this is one of the many reasons why relying on auto_prepend_file and other PHP-specific configurations is a bad idea. You simply must be completely aware and at the mercy of PHP's configuration in order to understand how your code works.
Instead, use autoloaders for loading classes and make sure you include your dependencies in code and not in PHP's runtime configuration.
P.S.: IDE's like PhpStorm can actually resolve functions by following includes in code, which is further reason to resolve dependencies through code rather than configuration.