Due to hosting setup requirements one may need to change the default symfony project folder structure to, for example, as follows:

/
  public_html/
    css/
    images/
    js/
    uploads/
    .htaccess
    frontend_dev.php
    index.php
  symfony/
    apps/
    cache/
    config/
    ...default symfony structure...
    symfony (script)

Note that the symfony sript is no longer in the root.

When attempting to open the symfony "Run command" dialog you recieve the following message: "Using the default symfony script because the project's one is not valid. (Symfony script is not a valid file.)"

So as a solution add the option to set the path to the symfony script (Or the symfony folder) in project properties in the case of it not being in the default location.