Essentially #127. The tag doesn't apply in-game because flower_blacklist.json uses an old Forge syntax.
Now it should look something like this, using the Vanilla syntax:

{
	"replace": false,
	"values": [
		"minecraft:wither_rose",
		{
			"id": "#botania:special_flowers",
			"required": false
		}
	]
}

(not actually tested, I used Craftweaker to apply the tag)