Is there a checkbox to get the discounted filing fee when filing a PCT Application as a *.PDF?

Yes. Checkboxes for discounted international filing fees are provided for in the "Calculate Fees" section of EFS-Web. If the international application is filed electronically without the PCT-Easy .zip file, the box "International Filing Fee (first thirty pages) - Filed in paper with PCT-Easy file or electronically without PCT-Easy file" should be checked. If the PCT-Easy .zip file is included with the electronic filing, the box "International Filing Fee (first thirty pages) - Filed Electronically with PCT- Easy file" should be checked instead to obtain an even greater discount.

USPTO FAQ - Questions and Answers (2007JUN01)