The threat level is particularly about how threatening and/or mysterious they are to humans. Note in particular how amicable Hina is, but because she apparently spread misfortune to everyone around her, her threat level is very high. Yamame also follows this pattern to some extent. They're dangerous, but because humans stay way from them their actual personalities are relatively unknown, and so the suggestions to avoid them are inflated.
Except Yuuka manages that level with her power being over Flowers. Not
illness or misfortune itself. There's a huge difference between someone whom touching would afflict you with Misfortune, Illness or Poison [Medicine] regardless of what they want, and Yuuka.
Plus her game personality is clearly... yeah. You're not sane if you are making threats about turning people into a mist of atoms as if you are joking, and 'Genocide is just a game'. I mean, she wasn't even provoked to go into Makai. The tourism wouldn't have bothered her, she dosen't even live in Gensokyo. She went there for the lols, and her 'game of genocide' was pretty much unprovoked.
And don't say that's her PC-98 personality; she's NO BETTER in PoFV. I seem to recall her threatening one of the rabbits with turning them into stew.
Yuuka Victory Quote vs Reisen:
If you thought I'd know without you even saying anything, big mistake.
It looked like you wanted to say that tonight is rabbit stew.
She's willingly happy to accept blame for the incident despite KNOWING exactly what the cause is. And thus have an excuse to fight.
Not to mention what Eiki says to her:
If you rest here, you'll become insane.
No, you might already be a little strange.
Whether it be humans or youkai,
or ghost or fairies,
you've attacked them.
Without much reason, as well.
[Yuuka]:
I was just teasing them.
It's a daily thing.
It is pretty clear that Yuuka is at best,
insane [Again, her reactions to things are violent and disproportionate, and Eiki strongly hints it, going so far
as to correct herself when she says Yuuka will go insane], and at worst, pretty darn close to her depiction in fanon.
Honestly; I find Fanon Yuuka to be one of the more accurate representations.