Cyrodiil queues fall under the umbrella of timed prompts, so yes those will flash.
Unfortunately addons will not have access to directly control the flashing. We want to keep the number of situations that trigger the flash very tight and specific.
That said, the flash will occur with whispers, timed prompts, getting kicked to character select (e.g.: afk) or login (e.g.: server down/connection), and entering combat (woops, I probably shouldn't idly browse the internet standing next to this World Boss spawn point @.@), all assuming the game window is not currently focused.
I can pass along the other things you're interested in but it's ultimately designs call.