When Alpha Threshold is enabled & set at 0, along with Refraction being enabled, GI seems completely disabled on Final Render output.

I may have missed it somewhere in the manual that they are not compatible and if so I think it would be a good idea to either grey out Refraction when Alpha Threshold is enabled or add a note to the Render area under Final Render letting the user know "Refraction is enabled, GI is now disabled or is diminished"

It's a guessing game enabling things like Reflections and setting opacity to 99 or less to activate it. Maybe as soon as the user enables reflections that it automatically adjusts opacity to 99 or lets the user know these tips, maybe in the message area that certain things need to be done or undone.

With Refraction toggled on disabling GI, I don't know if this is normal operation or a bug but maybe in the future you will make things more intuitive and give tips in the message system when users attempt to do things that aren't supported or let them know what they have to do to make a feature they're trying to use work correctly.