Hi - we have only noticed the issue on window create. That is, they should only steal focus one time.
There are a few reasons we draw our own right now:
We support Windows 7 (though this is less an issue over time)
We draw animated results in the notifiers (for instance, while dimming)
The interaction with native code and windows "modern" notifiers was a bit difficult when we wrote this (they live in two separate universes, or did at the time). For instance, at one point we were registered as a new "app" on every launch, and we filled up the SQL database Windows uses for managing notifiers with thousands of entries, all named "f.lux" - that was pretty upsetting for our beta testers.
#3 was the immediate reason we took this out but it is probably easier to make it work right now.