In the final assessment we have to remember several things, above all that Nimitz was aware of the context of his early statements as CINCPAC and their propaganda and morale value. And that above all he was still thinking how he would have expected the attack as an American admiral not how he would have done it as an IJN leader.

On the first point we can credit him with being essentially on the money. A generous portion of crews from the fleet was ashore that morning. But nowhere near 90%, but a noticeable amount. The evidence, even though for many ships exact counts are hard to come bye, is that any where able to get underway at all. Something just not possible without even enough bodies on hand. While the battleship Nevada is the most famous example, as the day went on several cruisers and destroyers did sortie as a ramshackle force. They were expecting to meet IJN surface forces and spent the next few days chasing ghosts. The core of this force were the cruises Detroit, Phoenix, and St Louis. One notable member of this force was the destroyer USS Blue which got to sea with only 4 Ensigns as her officer compliment!

And certainly if the fleet had managed to sortie with only Enterprise and some shore based air for protection against Kido Butai would have been extremely bloody for the USN.

On the second point we would be wrong to ignore both the actual facts of the attack(which Nimitz may not have wanted to put out there) and what the attack was hoping to achieve as the IJN understood it. There were two notable instances where the attack did hit important parts of the dockyard, which was essentially facing battleship row and Ford Island. First was that 1010 dock the massive pier that many ships could tie up to at once for quick work or loading before sailing had the cruiser Helena hit by a torpedo that could have sunk her in place. Only good DC and an alert crew really saved her. She happened to be unlucky in that the said position was routinely occupied by battleships and usually the Pennsylvania the flagship. So the location had high importance for air crews. Astern of her though the minelayer Ogala was much less lucky and capsized. She wouldnt be righted until April 1942 and dragged away in the summer of 1942. Pic from Wiki of the situation.

The other one then is the case of Dry Dock No. 1. The flagship Pennsylvania was there that day along with the destroyers Cassin and Downes, Both the smallboys suffered catastrophic damage despite attempts to flood the basin to prevent more fires. And while the battleship was removed the hulks of the DD's would stay there until late February 1942, greatly limiting the effectiveness of the drydock. It was still usable though and gives us this photo of the cruiser Raleigh in the first week of Feb. 1942 in there with the hulks Pic.

Certainly more damage could have been done. But if that had left a viable fleet ready to sail it would have been almost as bad from an IJN point of view as it would not have given them the freedom of movement without potential counter moves to complete their drive South. That most USN war plans called for a relatively conservative scheme of operations for the first few months of war anyway was not something they were privy too of course.

While on the final point its another questions of best using a very limited number of aircraft with a limited number of bombs and a huge number of targets. And frankly Nimitz is also overstating the damage a Zero shooting the tank farm up could do. While the tanks were above ground they were still pretty damn strong, only their 20mm cannons could have really punctured them, and couldnt get at the underground pipes. But for many of the tanks that just leaves a lot of soggy ground as much of it was full of Bunker Fuel for the ships. Unlike diesel or gas, at room temp its almost a sludge like compound that needs to be heated in the ship before it will even combust or flow. Now with some bombs it could burn of course, but thats a lot of work, though the fuel tanks with avgas or other petro chemical products could have really burned nicely. But even then stocks can be rebuilt and fuel barges used. The bigger limit was that the Pacific Fleet was reliant on about 6 fleet oilers for any operations, most of which could barely sustain 12 knots and were a much larger bottleneck! Ships on the bottom now or thirsty in a month or two is an easy choice when the plan is a lightening strike to seize territory then fortify and await a counterattack and hope for offers to negotiate.

There were many things that were compromises in the attack for the IJN, and Nimitz does note some parts that made things better in a way for the US, but is also very much making a propaganda statement here not 100% reflective of the actual attack or realistic possibilities.

Saw your EDIT: and there are a few additional comments I would add. And its sort of not shocking its written by an Air Force Major.

For instance this quote:

Professor Thomas C. Hone best stated this condition: The American battleships were all old; several were nearly overage; most were overweight. None of the battleships in Pearl Harbor was a first-line warship in a material sense; all had recognized deficiencies.

Ignores that they were for the most part still an effective counter in enough respects to their potential IJN foes to be a real threat. And of course the best part of a year still from any of the new Fast battleships of the NC and SD classes being ready for action. When they are all you have and the same basic vintage of your foes they are still your first line. Regardless of their viability in combined carrier task forces or in screens, which was still a secondary concern to all but carrier water holders like Halsey.

I would also say that by basing so much of his analysis on Prange, and by that way Fuchida, its still flawed and not in line with modern historiography. It makes numerous references to ideas like a viable 3rd wave, or Kido Butai staying in Hawaiian waters to draw out the damage. Assuming both tings were viable to be supported by IJN logistics, and the best use of precious few carrier decks.