Particularly since the batteries the Gigafactory will produce are not fit for use in consumer gear, at least not without heavy modification. Tesla uses them in temperature and load controlled battery packs, so they have stripped away all of the protective circuits that nomally protect LiIon cells from overload and even removed the outer metal casing thats supposed to stop them from shorting out.
The design of the current Tesla battery would have been significantly driven by the nature of existing capital investments in battery manufacturing processes. There's no indication that batteries would necessarily be in that form in a process you build from scratch. The Gigafactory could very well plan for variations around their core production process. And, based on the production volume that Apple could consume, Apple certainly has the investment capital to make that variation worthwhile.
Actually, Panasonic built a new plant. But thats besides the point. As you move to the kind of battery you would want mass-manufactured and used in Tesla battery-packs, the level of protection and isolation by each cell will only get less, not more. And you certainly don't want to deal with the pouch form-factor that is needed in devices like the iPad.
I see your point - but Panasonic's plant may still be constrained by current market demands. A new plant, and new Tesla car battery design can be driven by whatever constraints will bring down total price in the Gigafactory + Tesla consumption. I would think that getting to that goal could encompass a battery design with a structural enclosure with intra-cell and outer-wall protection for pouch batteries. Vs cylindrical cells with no outer wall protection it just doesn't seem like that large of an engineering jump - more of a repeat of the previous engineering design processes at a different design point.