Why hybrid battleship-carriers lose too much

Would the Ise-class hybrids have worked better with fighters and a deck-transfer arrangement?

No. Combining battleship and carrier roles sacrifices too much of each, so a proper carrier conversion is the more useful choice.

Warships built around battleship and aircraft-carrier roles sacrifice too much of each. An Ise-style conversion loses more usable gun power than the removed turret count suggests and still lacks the flight deck of a true carrier. A full conversion with an angled or nearly angled deck would be more useful, although the angled-flight-deck concept had not yet matured. Shinano, converted from the third Yamato-class hull, provides the cleaner model for the preferred approach.