Title! I've been bonemealing in the desert and all it spawns is grass, no flowers. I do not have anything blacklisted.

I've noticed this too when working in Badlands. I assumed it's because deserts & badlands don't naturally spawn flowers.

The mod only changes existing flower spawns, indeed because deserts and badlands don't spawn flowers it can't randomize them. As this is Minecraft's intended behaviour it's not a bug. Thanks for giving the mod a try though!