Nothing in the incident report suggests the pilot's life was at any point in imminent danger, with the backup instruments functioning, and the plane being flyable.
He "technically" did well to eject only because the manual was too vague. But at the very least "I could have done more but technically didn't have to" is not what you're looking for in a squadron commander. Which is why he's still allowed to fly (he follows the manual) but not trusted with more than that (because those extras are not in the manual).
Maybe I'm going out on a limb here, but I imagine the most straightforward explanation is the correct one - he ejected because he didn't feel safe flying this aircaft anymore. I cannot possibly imagine that any pilot would eject from an aircraft they felt comfortable flying, given that actually ejection is horrifically dangerous and is very likely to maim or kill you, with most pilots unable to return to active duty after ejecting. He wasn't sitting there going "well the plane is flying fine, but the manual says to eject so off I go I guess".
Ejecting from a plane is dangerous. If you have control of the plane then you should be looking to do an emergency landing - there are typically acceptable landing places all over that can get you safely to the ground. I don't know how much control he really had, but it sounds like he had enough to land.
Tbf, the article describes them as "basically functioning". As someone with avionics experience, there's a lot of wiggle room in the word "basically" and I'd want to know the details about the remaining functionality before drawing any hard conclusions.
There's a big difference between seeing the report in hindsight and being in that aircraft at that given time, having lost your HUD and electronics a couple times already, not ejected and carrying on for a while before deciding its probably too risky to continue operating the aicraft.
How would that pilot know for certain the aircraft was still flyable? That it technically was at that moment is absolutely not the point, and is only known retrospectively after analysis.
I unfortunately don't have anything to confirm that, but I wouldn't be surprised that the fact that it was an F35 didn't help that man's case, as in losing a cheaper piece of equipment would have been less impactful.
I'm pretty damn sure he was thiking about the manual when his controls were glitching and decided to eject. Which also carries risk: his helmet and mask were ripped off and he had to drop the seat pan and raft in order not to get tangled in the power lines.
The Navy's contractors should sort out the glitches in their expensive space junk or build UAVs instead. What if this was a real combat scenario instead of an exercise, where the pilot didn't get to call 911 and risked getting captured by ISIS or some other maniacs?
He "technically" did well to eject only because the manual was too vague. But at the very least "I could have done more but technically didn't have to" is not what you're looking for in a squadron commander. Which is why he's still allowed to fly (he follows the manual) but not trusted with more than that (because those extras are not in the manual).