It's unfortunate, but I do not think there's a way around this issue - or how some chat messages won't be delivered either - without Wube providing more API possibilities. The best way to role-play this is to imagine you're so "in-the-zone" while designing blueprints in your mind that you forget reality exists. I'd like to solve it, but that's how I think of it for now.
For many features of this mod - more recipes, all technologies, multiplayer, and Space Exploration support to name a few - it's necessary that you are swapped to a different Force inside the Sandbox. Since those Alerts are based off of their owner's Force, and there's no way to get those Alerts or send them to other Forces, it's a necessary tradeoff for now.
