Using Ubuntu 17.04 and gnome-shell 3.24.1-0ubuntu on an HP laptop with an ASUS screen, I have the screen to the right of the laptop on the desk and set back so that *visually* the ASUS screen appears to the right and about 50% up from the laptop screen.

On the Unity desktop, when the Display configuration is set to the ASUS rectangle is moved up from the baseline of the laptop screen rectangle, there is a seamless path for the mouse to travel from one screen to the next, up at an angle, the cursor exits at 75% on one screen and enters the next at 25% of the height, a very natural movement.

This does not work with Gnome-Shell: no matter how the rectangles in the Display system setup are aligned, if the cursor exits one screen at 25% of the height, it will enter the other screen also at 25% of the height, which is no big deal, but it is annoying and all the more so because it works as expected in the (deprecated) Unity desktop.

Further to this, if the rectangles in the Display setup are set with the
base of the right box slid 50% up the side of the left, the cursor will not
move right beyond the lower 50% of the laptop screen or move left of the
upper (non-overlapping) portion of the ASUS screen -- the cursor stops dead at the boundaries (as could be expected) however, in the overlap boundary region, the mouse will enter the neighbouring screen, but jump to the same proportional height as it was on the prior screen, ie it is moving as if the screens were set horizontally flush aligned instead of continuing the smooth path across space.

What I really expect to happen, when the Display rectangles are arranged where both are 800x600 and the right screen set 50% up, then the total virtual deskspace would be (800+800)x(600+300) ie 1600x900, with bounds from the top-left of Screen 1 from (0,600) to top-left of Screen 2 at (800,900), and from bottom-right from Screen 1 (800,0) to bottom-right Screen 2 (1600,300) allowing the smooth trajectory of screens, cursors etc across the space between the screens.