Popup in the middle of Transactions

Are you referring to the overlay that shows when you grab the scrollbar on the side of the window and scroll? If so, no, you cannot turn that off. However, that overlay does not appear if you simply scroll using the mouse scroll wheel or 2-finger scroll on a trackpad. Nor does it appear if you use the keyboard page down/up keys (fn-down/up arrow if you don't have an extended keyboard). I'd suggest using those scroll methods if the overlay bothers you.

AFAIK, every Mac keyboard has an fn key. What model Mac are you using? If you are using an external keyboard, is it made by Apple or third party? If you are using an extended keyboard (one with a number pad), there should be a dedicated fn key as well as page up and down keys between the alpha keys and the num pad.

As for using the arrow keys by themselves: if the last thing you clicked was one of the accounts in the sidebar, then yes, the arrow keys move up and down the account list. However, if you click on any transaction in the register (highlighting it in blue), then the arrow keys will move the selection up and down. If you hold down the arrow key, it will repeatedly move the selection up or down, scrolling the screen as necessary. The speed at which this happens is controlled by the Key Repeat Rate setting in macOS Settings > Keyboard.