As I previously mentioned, the "spinning circle" cursor error is a bug in Godot engine, so you could probably wait until Godot 3.1 is released, and use the code you were previously using. Alternatively, you could try to take advantage of the fact that the issue is resolved if the cursor exits and re-enters the window by using the following code:
func _on_BottomBar_mouse_entered():
Input.set_mouse_mode(Input.MOUSE_MODE_VISIBLE)
var curPos = get_global_mouse_position() #Save position where cursor entered the Panel
get_viewport().warp_mouse(Vector2(-50, -50)) # "Teleport" cursor outside of the window. Any position outside of the window will work. (-50, -50) is merely used as an example
get_viewport().warp_mouse(curPos) #Bring cursor back to its original position
Note however that this is more of a hack than a fix, and it will not work if the window is running on full-screen mode, though it should work if the window is simply maximized. Furthermore, you will probably still see the spinning circle for a split second the first time the cursor enters the Panel, after which point it will default to its intended behavior.
Edit: After some testing, I noticed that warping above the window might not work if the window is maximized. An alternative solution would be to warp below the window, so that the cursor temporarily goes to the taskbar (e.g. by using Vector2(OS.get_real_window_size().x, OS.get_real_window_size().y + 20)
instead).