Except the very first bullet point at the top of the page says it doesn’t include the bonuses if you are upgrading. I’m sorry you missed it, but it is stated twice on the page, at the top and bottom.
If you feel like it could have been clearer, you can always submit the feedback in game or on the General (or maybe website?) forms. The feedback won’t be passed along from this forum.
You can also look into getting a refund for your upgrade purchase, it sounds like you may not have used it yet since you didn’t have time.