For some reason, this is just how sections load in this game. It's far better to fly straight above where the checkpoint zone is so you fall into it. I'd check Erims' run for a great example of this:

As for the subpixel/nudge lineups, if they work for you, hey all the power to you! However you have to be careful about losing time doing the lineup each time the nudge fails. So in order to get it as fast as possible, you are much better off getting roughly into a position where you only need to tap a few times. The reason there is no 100% guarenteed setup is because it is highly impacted by human error; no human can tap down a key for the same duration every time without fail, if that makes sense? The rest of the setup once you are in the .282 subpixel is deffinitely consistent though!