Came here about this issue as well as dimming being disabled when opening settings and every time the settings window is switched to the display "tab." This setting fixes the notifications (which oddly only seem to be bright the first time they're opened in a while, but closing and reopening the bar reactivates the dimming) AND the settings window issue, so that's great.
As for you reasoning for not enabling the option by default, I highly doubt leaving it broken is going to encourage MS to fix their crappy OS. There are still numerous minor bugs that have existed for years. And they don't even care about security issues (often ignore ones reported to them until the discoverer of the flaw goes public) and serious bugs, so something minor like this will likely not be fixed for years, if ever, and that's assuming they're even aware of it. Plus, they have their own version of this (Night Light), so that makes it even less likely they'll bother fixing something that's an issue for f.lux. It's just not worth bothering users in the misguided hope that it will lead to MS fixing things.
Also, off-topic, but I'll mention it here instead of making a new post just for it: The text in the main window that says "The sun has set. Light is making your body later." doesn't make any sense and has always bugged me. I've just always assumed whoever wrote it is ESL or used a translator for it and that it's trying to say something like "The sun has set, light will delay your sleep cycle" or "The sun has set, light will disrupt your circadian rhythm."
