I agree with this decision.
Firstly, Yukari Yakumo is the
only Phantasm Stage Character of the entire Touhou Series.
Every single Touhou Game features 6 Stages and an Extra Stage, with the sole exception of Touhou 7: Perfect Cherry Blossom, where Yukari Yakumo is the Boss of a secret 8th Stage.
Secondly, then nature of her Reality Warping powers and her status In-Canon as one of the most, if not the most powerful Youkai should do her credit. It is ridiculous to think that a Stage 6 character would be more powerful than her.
Thirdly, Yukari isn't equal to Suika. One needs to understand that Yukari is the type of character who is very laid back and casual about everything. And furthermore, Yukari did fight Suika, this was the result:
https://www.youtube.com/watch?v=-xdr2Cs4FGQ (17:40 Fight Starts, 22:30 fight ends)
Neither were serious, it was a sparring match. However, Suika's sprite is bruised after the fight, so there's that.
Also, Yukari has used her Boundary Manipulation to make it so that it was night and day at the same time.
Edit: Other things.
Here we have this quote:
"I'm a youkai with the ability to control the boundaries between any and all things. This power allows me to remove the boundary between anything: Gensokyo and the outside world, the worlds of the living and the dead, humans and youkai, even day and night."