The Tsuchinoko is a creature that manipulates plants.
And Yuuka has the Manipulation of Flowers. While Flowers are plants, plants aren't strictly flowers.
Very late, but regarding Yuuka only being able to manipulate flowers, not plants as a whole, Yuuka could theoretically manipulate any plant that can grow flowers. They're connected after all, so Yuuka could exert her magic and power via the flower into the rest of the plant. Thus, Yuuka could control many kinds of plants and trees, though not every plant (plants that do not grow flowers are out of her control). So she could count as a plant manipulator, like Suwako.
Also, two interesting tidbits I noticed in her
Perfect Memento entry:
"Completely unrelated to her abilities, she uses her umbrella and scatters flower petals to perform graceful attacks. "
"The ability to manipulate flowers is something to the extent being able to make flowers bloom, shift the face of sunflowers towards the sun, or make withered flowers bloom again. This ability is more of an extra;"
This, combined with the 'ultimate magic' stuff from Mystic Square, implies Yuuka might have more tricks up her sleeve than just flower manipulation.