What would be interesting and I will test is this: what if you delete waypoint as soon as the second stage kicks in? This should force the algorytm to find a new target through the active sensor. Now if that doesn't work it means you have a sensor rerouting bug.
If you launch first the same missile design with a buoy instead of a warhead on the second stage then you have your targeting ready for u to shoot long distance. In this case, you will be able to target the specific enemy ship. I would keep the active sensor on the missiles just to have a backup in case your buoy get destroyed but you could consider removing it to gain speed, range, agility...any of your liking. If you go for that you may want to deliver 2 or 3 buoys first.
So I tested the above and it doesn't work. You'll have to do it long range but still in the range of your Missile Fire Control and shoot directly at your target using the Active Sensor of the Buoy. When it doesn't work I meant missiles get fired fly to Waypoint correctly launch the second stage but then don't reroute to target but still going towards the Waypoint even after have cancelled it.
You can still invest in a very long-range MFC, the problem is the weight. I've compensated using box launchers at max. The other problem is the speed, you need to ensure your last stage is over 20,000 or everything will be shot down. I have also used the Sync Fire to make my salvos bigger and get more chances to penetrate PD.
For the sake of the test I capped the ships at 10,000 Tons, 6 months deployment, no jump engines, maintenance and fuel realistic (3 years, 160 days @2,000km/s). Tier 3 techs, Ion Engines. I think it is pretty solid as you cannot use these ships earlier.
I fired at 585mkm in my test game, however, the buoy has been fired at 5b km distance.
IMPORTANT NOTE: I am sure this is WAI as I can see how it could be cheating and not realistic otherwise, ff this would have worked, the MFC would have been pretty much useless.