This is actually Apple's fault more than anyone. I was originally planning to release on the App Store but decided not to after thinking about the $100 a year fee to be in the developer program and the 30% cut Apple would take if it were paid, and that's assuming the app would be approved by Apple in the first place. Although I decided not to release on the App Store I want to keep the option open. Apps on the App Store need to be sandboxed, which means no preference pane.
I agree apps filling up the menu bar is annoying, so there is an option to hide it if you wish.
Looks like it, yes. I don't use any special private APIs, just the public ones that you can use in apps on the app store. They need the accessibility permission to "Control your computer". Apps like BetterSnapTool/Magnet work with the same permission. Here's the code that actually intercepts scroll events: https://github.com/ther0n/UnnaturalScrollWheels/blob/master/...
I agree apps filling up the menu bar is annoying, so there is an option to hide it if you wish.