Colin, the shots you do post are pretty magnificent, so obviously it CAN lock accurate focus.
Speaking for myself only, I shoot a lot of birds in flight, and have been there for several years. Yet, my success rate is still pretty low. And those whom I have shot with, report the same thing. Are you perhaps expecting too much?
Anyway, I also use a D500, although with a longer lens than yours (500mm f4 G). My settings are pretty involved, but basically:
Exposure mode manual, but with auto-ISO. Lens typically wide open unless there is LOTS of light, and I definitely find that a higher shutter speed increases the percentage of sharp photos. Under 1/1000th, I get almost no sharp shots except with very large, slow birds. The tiny lightning-bolts like the smaller Kingfishers need more than 1/3200th when moving.
My AF settings are very intricate, and in this regard I love the user-customiseability of the D500. I use back-button focus exclusively, set up as follows:
The AF-on button gives me 25, 72 or 153 points (selecting between them as conditions change).
The pressing the joystick gives me single-point AF. I use this for stationary targets (perched birds), as it allows me the fastest way to also move the focus point around while focussing.
The Fn1 button is set up to change the AF area mode to Group Area, but not to focus. Thus I change the mode using my middle finger, and focus using the AF-on button.
The setup is used as follows:
For perched birds and general wildlife, I focus and control the position of the focus point using the joystick.
For birds flying against an even background (the sky or smooth water) I use the AF-on button on it's own.
For birds flying against a busier background, I use two fingers to get Group Area.
In this way, I can change between those three basic focus modes seamlessly as the bird swoops above or below the horison.
I do still want to experiment more with 3-D tracking, as I have not really tried it on birds with the D500. With the D750 and D7000 I used to have, it was effectively useless, but on the D500 I have used it with face detection on models in studio, where it worked very well.
I hope that rather long-winded explanation helps somewhat?