This requires two things: an understanding of the limits on existing logistic capacity, & an understanding of the threat from submarines.
Japanese leadership had neither.
The reason that Militarst Japan didn't have enough transport ships (other than the fact that their economy was far too small to allow them to build up everything they needed or wanted) was because the "short war" school won in the 1920's. There was a big debate in the interwar period between those who argued that any future war that the Empire of Japan found itself in would be long and industrialized, and those who argued it would be short. The "long war" side argued that Japan should build up transport facilities, industrial capacity, and resource stockpiles, and pay for all of these by having a significantly smaller standing army. Then, if and when war came, it would be easy enough to quickly build up the military through calling up reservists and conscription. The "short war" side argued that long wars like the World War were unlikely, given Japan's likely enemies, and that at any rate if the Empire did fight a long war it would be beaten anyway. They argued for the need to keep large numbers of troops under arms at all times, for quick decisive action.
Of course, in OTL the "short war" side won. There are many reasons for this: it played into the ultranationalist/mysticalist notions of the primacy of elan, the zaibatsu tended to support it because it lead to higher military spending and less government control over production in the short run, some civilian leaders supported it because a larger army helped keep down the numbers of unemployed young men. But by far the most important single reason was political. The Militarists knew that their power base lay in radicalizing the rural poor. The more soldiers they had under arms, the more support they had for Militarist policies, simple as that. Before the complete takeover of the government by the Militarists, when the Army was just one power block among many, this was their overriding concern. Of course, when the Army was able to push this through, the Navy had no choice to join the "short war" side, too. If they did not expand their numbers at the same time, they would risk being rode roughshod by the Army. Building more warships adds to their numbers and power, building transport ships does not.
The bottom line is this: your idea that the Empire of Japan didn't build transports because they didn't think logistics were important is a gross oversimplification. The lack of sealift capacity was an unintended (but forseen) consequence of the strange political realities on the ground in 1927-1945 Empire of Japan. It is not impossible, or even implausible, to design a PoD or two that would change this, allowing Japan to build much more transport ships.
Forget ideology. This was an IJN doctrine issue, & was symptomatic of the grip Mahan had on all major navies prewar: namely, guerre de course couldn't win a war, only battle between gunlines. IJN bought it.
Unless you change that, you don't change the number of DDs built.
You then have to overcome the incapacity to grasp the need for better sealift & better trade protection... And you need officers who know the difference between tactical & strategic victory. Japan didn't have them.
In short, you need better educated senior officers going back at least 20yr.
You just need the "long war" school to win the debate. They believed in a decisive battle because that's how the short war would go. "guerre de course" is a long war strategy. If the long war is planned for, it will be included.
So why didn't they OTL?

Because it didn't effect them. It's easy to ignore the effects of a blockade if it only happens to someone else. That's why my suggested PoD was for a Imperial German commerce raider to target Japanese ships in WWI. If the Empire of Japan faces this issue itself, then of course they will pay more attention to it. That gives them a reason to look at how other Powers have been affected by this issue (including Great Britain's experience with subs), and the responses they have developed to it.
That seems to require more engineering depth than Japan had...
Turbosuperchargers require more "engineering depth" than the Empire of Japan had?
In 1945, the Empire of Japan had lost huge chunks of their industrial capacity to bombing. The factories that were still able to produce couldn't, because the power grid was damaged. If they had power, the destruction to the transportation grid made it nearly impossible to bring in coal and ship out steel, etc. Despite all of this, they were still able to produce a working jet engine based on nothing more than a few German photos and a cut-away diagram. The
Kikka flew before the war ended.
Given all of that, I think they could manage to built a workable turbosupercharger back when their industrial base was intact, given that they captured several Allied planes equipped with them. After all, what is a jet engine except an incredibly advanced and complex turbine?
As to why they didn't manage to historically, who knows? Why were the Americans able to engineer and produce the incredibly advanced B-29, but still couldn't produce a good enough engine to drive the Mustang without just copying a British design?
These are all changes that require 747-size butterflies by 1940, or changes going back a generation or more.


They look small to us, 'cause in the West, we did it. Japan didn't, because she couldn't.
This would be big PoDs by 1940, yes (except the turbosuperchargers). That's why you may notice that one of my PoDs was in the mid-1920's, and the other one was in 1914.
Not a chance. Japan couldn't have survived past mid-1946, not with mass famine on the doorstep. And "the lives of nearly an entire nation" is nonsense. It's Truman's justification of the needless use of the Bomb.
For once, I agree with you. The whole idea that "if not for the bomb, it would have meant invasion" is just an idea promoted to make the strategic bombing look modest and reasonable. If the bombs had not been ready, then the Empire of Japan is most likely starved into submission before the end of 1945. The dropping on sea mines into inland Japanese waterways and canals almost guaranteed starvation by itself, since it blocked the last remaining way for the Empire of Japan to move food from the countryside to the cities. The bombs might have actually killed fewever people than would have starved that winter, it's hard to say. But there would never have been an invasion.