You make a good point about the inability of Japan to realize its ability to produce more advanced tech, due to their destroyed and under supplied industry. Like a poster above said, while the game mechanic may mimic the fact that Japan could not catch up in research, it is not fair to say that Japan did not have the ability and as such should not get a permanent penalty.
If Japan's research could be held back, how can that be added to the game so that any country's research could be held back, just as well? The developers could reduce research speed for ALL NATIONS by the same percentage of factories a nation has damaged and out of use. So if a nation has 100 factories and 10 are being repaired, that nation receives a 10% slow down in research speed.
This way Japan, or any other nation, would not suffer the slower research speed they had historically unless the Allies actually spend the time, effort, and resources to reduce that tech speed. This way the Allies do not get the free cheat against Japan. They must pay for it and it would work on any nation equally as well.
I understand Japan had other disadvantages they were dealing with, like how it only took 300 plus B-29s in a single mission to create firestorms in a city that equaled atomic bomb casualties and destruction, but that is a separate problem to simulate. The above might help with the research issue. Japan was very capable, but if the Allies were willing to pay the price, Japan suffered research and production disadvantages.