Well, technically, since the school festival is still going on, (I believe) the flow of time is still unstable, so there are some inconsistences even when the past was changed to our current present. So yeah, things are still kinda jumbled up. It's possible that some things still reflected the past were left unchanged even when the Clock Keepers changed the past.
And, I'm pretty sure in the very beginning, Hanako noticed that Kou didn't know how to control the power of Raiteijou, so he basically put the seal on for his own good. It's possible, over time, Kou learned to control it better, and regain the power that was sealed up somehow, channeling it in his own way. If you think about it, the seal just kinda acted like some sort training wheels if you will. And as time goes on, you don't need the training wheels as much and you can become steady. Even so, I'm pretty sure the times that Kou used Raiteijou it wasn't to its full extent, the seal still retained its true power. When Kou used it in the beginning after it got sealed, there wasn't that much power in it. It's possibly because of his skill-level back then, and as he went through many other events, he got stronger and improved his skills. So he was able to use Raiteijou more at ease.
Hope that helped explain things! (I actually just helped myself too wow)