Noel,
I don't know how many courses Alison did in Japan but I assume it was a relatively small number, say 5.
Given WWII and everything else that has taken place since those handful of courses were built, and given what we have seen happen here in the U.S. by well intentioned club boards, a fair amount of work is likely to have been done to Alison's Japanese courses. For example, it definitely sounds as if the greens were flattened at Kawana at some point based on your descriptions.
And let's face it - why would his courses be immune to the actions that struck all the other great architects around the world?
And when there are only 5 or so courses to pick from, you can't fall back on sheer numbers figuring that there is bound to be some unspoilt gem amongst them.
I don't know if the above logic is correct but if it is, I doubt if Kawana, Hirono, Nauro,Tokyo GC, etc. deserve their high world rankings in GOLF magazine. For instance, I don't get the sense that you would place Kawana #58 in the world - is that true enough?
Cheers,