Yes, it's not just the 'structure'. It's the heat dissipation, which is axial in 4680s (cooling from top and bottom), while cooling is radial in 2170s (cooled by contact with the side of the bty can). It won't be trivial to design two different packs that fit in the same space, and share cooling connections.
I think its more likely Tesla just puts tabless 4680s in the Berlin Y, and accepts the best available level of bty tech wrt the other aspects of optimization, like anode/cathode chemistry, materials sourcing.
Cheers!