You can still speak with Siri to trigger HomeKit scenes when in Auto mode. Auto mode simply has your ecobee assume the default temperature range (between your heat and cool set points) of the comfort setting. For example, asking Siri "set my temperature to 72F" will do just that, with the default temperature range of 5F. We chose 5 degrees so your system doesn’t constantly switch between heating and cooling, helping you save money on your energy bill.
Here's more information on heat and cool set points, with instructions on how to change them.