You have always been able to discount time period fee, but not if that time period fee was a part of the fiscal year fee. Now you can discount the registration fee even if you are using the fiscal year time period configuration.
To make your fiscal year time period fee discountable go to Find > Time Periods. From the View drop down menu, choose Fiscal Year and select the fiscal year you wish to make discountable by clicking on Edit link. A modal window will open where you can configure fiscal year name, date range, fee, and if you wish or not to make it discountable. To make that fiscal year fee discountable, just check the box "Is Discountable " and click on Update to save the changes you just made.
Now, any time period fee that is under this fiscal year umbrella will be discountable. However, you can change this form term to term. For example, if your organization has four terms within one fiscal year, you can make one or two terms discountable and the rest non-discountable by just updating this "Is Discountable" check box.