The ending was a bit rushed for Tokujira, but Itsuki ending up with Botan totally made sense with all their romantic developments since ch 11. At a certain point Itsuki's feelings towards Tokujira became more like Botan's feelings towards her (wanting to help their friend overcome her flaws) instead of a romantic crush. Meanwhile Itsuki and Botan really does have that chemistry together, Botan willing to look past his apperance and mistake to see his good intentions and they share similar interests with him too. It just make sense for them to be together.
Not all's bad for Tokujira though, despite being a third-wheel in a lovey dovey couple, she's still pretty close to both of them at the end. Their dynamic remained almost the same, just with Itsuki and Botan now dating.
All in all, a cute romance manga with pretty solid writing (could've delve more on the cross-dressing thing or polish out Tokujira's backstory though).