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A simple solution:
at some point in time, there is commissioned only empty ship hull. Player have option to make two conversions, either into CV, or BB.

Now, if it would be possible to put ship back into production queue(similar to WITP conversions), all would work fine. But I can not find such options. Both, upgrade, and conversion put ship into repair. So the other option is to actually produce this hull near REAL commission date. This gives Japan player more flexibility, but at the end of 1944, that should not change much.

I see, that she was supposed to house 139 planes. But most of them should be only refitted.
So...
if it would be possible to actually equip the ship, with REPLACEMENT SQUADRONS (as I understand Japan have none of them), that will make it actually worth, to build Shinano.
The second option, will be to actually give her this 139 planes capacity.

Are Replacement Squadrons universal, or does only Allies can use them?

Well, it seems there is additional field, for checking replacement squadron, in editor, so this is actually pretty simple modification. I hope it works for Japan: