A beekeeper here.

1. Bees have only been kept in flat frames for less than 200 years which would not be enough time to select for such a specific trait.

2. Domestic bees that swarm and find homes in hollow trees or gaps in houses form blobby swirls of what beekeepers call 'crazy comb'. The liberated bees create topological forms which are probably much more efficient than flat frames. Flat frames benefit the beekeeper, not so much the bees, and bees will make comb when and where they like.