Its not my opinion. I’ve forgotten now the source, perhaps it was Garzke and Dulin’s definitive work, but the writer posited (with a detailed explanation) that the Mitsubishi yard was superior to the Kure naval yard, in the skill of its workforce and construction techniques.
Kure still turns out the gunboats and lesser naval craft; Nagasaki the more high tech stuff. So I stand corrected.
However, I still think the nature of the missions, their fuel and their crew size also played a large role.