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In explanation of this baraita, one suggestion that is raised (either by Rav or by Rabbi Yehuda haNasi) is that pat ava does not mean to bake a thick cake; rather it means to bake a large amount at one time. The Gemara points out that if we understand pat ava this way, the potential problem would not be specific to Pesaḥ, but it is a general issue of possibly baking unnecessarily on Yom Tov.
Rabbenu Yehonatan explains that if this is, in fact, the point of disagreement, Beit Shammai forbids it lest some of the bread or matza will be left over and will be used after Yom Tov is over, creating a situation where preparations for the regular weekday were done on the holiday. Beit Hillel would argue that the baking process works better when a large amount is baked, so having leftovers is of no concern.
These concerns lead to the discussion of the shape of Matza, round vs square and the 19th century controversy over machine matzot.