Your body “tests” what you eat long before it gets digested; otherwise it would defeat the purpose of testing. You check identification at the door, not when you’ve already let someone in. If you digested dangerous foods, the toxins would enter your bloodstream.
I’m not sure I agree you necessarily feel better before you’ve expelled it all, but the “testing” happens at the front end; once the food goes further downstream, you react to it less. It still won’t be comfortable – your gut bacteria won’t like it – but it’ll get taken care of.
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