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But how would she pee accurately from up there? It would just splash down everywhere, no?
Is it weird of me that the first thing I thought when reading this was "It didn't really have to alter the eyes; the brain is actually pretty good at handling weird input and she'd probably see things 'normally' after just a day or two."?
Nope, you're quite right. Neuroplasticity for the win. If anything needed to be inverted, it's the structure of the inner ear.
The answer to all these questions and more is "clearly the Matrix isn't familiar enough with humans to get all the details right."
...Except that would be dodging blame. I just didn't think of everything at the time... but hey, that's what the "Matrix keeps making changes" option is for!