I see a lot of over complicated layouts. Something tried and true would seem better to me:
On the map, RTS controls: Click to assign a destination, or cancel a waypoint course; Shift+click to create a waypoint course.
Campaign view, same as it is currently with one added trick: Click to assign a normal destination hold click to fly around, and either
A Hold click to also maneuver the fleet
without cancelling a waypoint chain, while click cancels it. Only problem with this is that if you want to cancel a course while dodging a fleet, you either have to pause the game to click and cancel, or loose a bit of speed as the fleet will try to resume course for a fraction of a second.
or
B Click to add a
single point in front of the waypoint chain. Clicking again always replace that single additional point, the chain itself stay unchanged. You can click close to your fleet to resume your waypoint course as the additional point is reached immediately. Hold the button for a second to cancel the waypoint course. This avoids the issue with resuming the course, but is slightly less intuitive.
Obviously only one of these should be used.
Note that if after altering the course or when reaching an added waypoint the fleet is closer to a following one of the chain, farther chain waypoints should automatically be removed. For example in the last image, the visible normal waypoint should be ignored since the added one is closer to the following one out of screen. This should only be the case with the added point, and it look different to avoid any surprise.
Just like a RTS... This doesn't change the current system at all, only add new functionality.