Japan's distance running times are not poor, period. They wipe the US for depth of quality times 5K and up. "Poor for the amount of training they do" is not something that matters.
Your #1 is cultural to the extent that it is true.
Your #2 is complete BS - there's no evidence that high metabolism is bad for distance running and there's no evidence that Asians have higher metabolism other than not being as fat. There are some that aren't super skinny like Yuki, but there are also wisps like Shitara.
Your #3 is probably wrong and also irrelevant. Someone all/mostly slow twitch doesn't make the best distance runner. In any case, I'm Chinese American and more slow twitch.
Your #4 is something that is overrated for running, and, in any case, the spread for the Asian dots on the graph you link pretty much covers the gamut (especially considering the large population pool) except for Aus/NZ (not sure what PNG is). I'm certainly not short legged, and my brother is long legged and tall. Anecdotal, but the Ginger Runner's wife's Japanese American wife's online name is "mile long legs".