Why no A-140 design solves Japan's yard limits

Which rejected A-140 design would have been a better choice than the Yamato class?

None, because the entire design family depended on shipbuilding infrastructure Japan did not actually build.

No A-140 alternative offers a practical improvement on the ships Japan actually built. The designs assumed yards and supporting infrastructure that Japan planned to create rather than what it already possessed. Similar infrastructure had been promised to make the Yamato program more practical, but it was not delivered at the required scale. Japan could barely construct the historical ships, so selecting a different paper arrangement would not cure the industrial mismatch.