This is a textbook example of ass-covering by the brass or even cognitive dissonance to the Nth degree. The report clearly states that initial AAR and SEAD sorties must be demonstrated to students/trainees in daylight conditions before attempting them at night, and yet this unit authorized both of those details within this single sortie, having compounded their error by mis-rating the risk assessment prior to the authorization.
OK, so far the unit has only flagrantly disregarded the safety rules for flight authorization. But now the holes really start to line up...
The Mishap Pilot (MP) (unsurprisingly) fails to refuel, so his SEAD detail can't be completed so he and his Flight Lead have to RTB. Approaching Shaw AFB the Flight Lead makes a remark to the MP “that was not the way to start your tanking experience,”. So what? This guy thinks he's screwed up, the sortie is a bust, and now his Flight Lead is confirming his suspicions even before they are safely on the ground. Nobody will ever know what went through this guy's head on that approach, but he was not able to employ the correct techniques for a relatively simple ILS recovery and hit the undershoot, trashed the gear and got it back into the air.
This is where the system really failed him. The Flight Lead and the ground team tried every way they could to make the emergency fit the checklist for "Landing Gear Unsafe". It wasn't unsafe, it was hanging off the aircraft and they knew that, but they either consciously or subconsciously avoided the "Ejection" option. There was an opportunity to get engineering advice from Lockheed Martin, but that was missed. Subsequently, the approach end cable landing went almost exactly as you could have predicted, and the MP realized he was in trouble and initiated the ejection.
The next event was just a tragic reminder of when your day goes bad, it goes really bad. The failure of the ejection sequence is what ultimately killed this guy, but to find there was an outstanding seat modification that had not been completed and multiple extensions to a seat component that was past its planned life were just more indications of holes in the maintenance policy for a critical life-saving component (not unlike the Red Arrow seat incident).
There were multiple opportunities to break this chain of events and gain a more favorable outcome for the Pilot, but they were all missed. So when an Air Force 2-Star says;
"I find by a preponderance of evidence the cause of the mishap was the MP’s failure to correctly interpret the ALS and identify the runway threshold during his first landing attempt"
You know that Careers are still more important than lives.