There are certainly theoretical limits, but it's probably so high that it's not relevant in practice. Let's say if you were eating for 100,000 kcal (without puking!) then yes of course your body would be unable to digest and metabolise all that. But for 10,000 kcal you should not observe a visible drop in efficiency of those biochemical mechanisms.
You don't pee calories, for a healthy individual it never happens. Pooing some can happen, and it usually feeds the flora of your intestines. But it's typically small quantities, most of the nutrients are absorbed in the very first centimetres of intestine.