Pills are too small to trigger the swallowing reflex, so you have to swallow them manually, when you eat food you take enough of a bite to usually fill your mouth somewhat, you chew and process the food in your mouth, telling your brain that you are about to swallow food, when it hits the back of your mouth, nerves get triggered that make you want to swallow.
A pill does nothing of that, it is a small object you have to conciously swallow and it is simply not a very natural thing for us to do.
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