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Well, those are some bizarre changes. Care to explain, especially the seemingly random third breast? And how the heck does she not make solid waste anymore? If she eats, like, a big ol' rock, is it just going to dissolve and be expelled as pee? Crazy.
The Matrix is (1) very alien, and (2) broken. Some of the changes it makes will be effectively random and may not make sense. Hence the third breast.
As for swallowing a large rock... why would anyone do that? Passing a rock would be unpleasant even with normal biology. However, since it has come up, some possibilities immediately come to mind:
(A) The Matrix has enhanced Sayaka's remaining digestive organs such that they can liquefy anything she ingests.
(B) In addition to the physical changes, Sayaka's understanding of what is edible has been changed as well. She won't intentionally eat anything that would have originally made her produce solid waste, and if she tastes something that her new biology can't tolerate, she'll find it absolutely disgusting.
(C) Sayaka actually cannot adequately eliminate her waste and is going to die of poisoning eventually. That's horrible, and I'm not going to write any episodes where stuff like that does or has happened.
That last point is darker than anticipated.
It's not a direction I intend to go or play along with, and I'll gladly go to great lengths to handwave it away in actual episodes, but it is nonetheless a direction the story could reasonably go.
I mean, it'd suck all the fun out of weird transformations as far as I'm concerned, but someone else might feel differently.