I think you're conflating "natural" with "familiar".
Here are two processes Timmy could use to count the pens on his desk. (I have numbered them starting with 1, because I considerately adapt to the needs of my audience :-).)
1. Say "0". Then increment for each object. So he goes: zero, (points to pen) one, (points to pen) two, (points to pen) three.
The advantage of this is that you don't need a special case when the number of pens turns out to be zero. Hey, Timmy, how many unicorns on your desk? Timmy starts by saying "zero", looks around, no unicorns, finished: it's the same process as for pens, it just stopped earlier.
2. Number the objects from 0, and then the count is the next number after the ones you listed. So he goes: (points to pen) zero, (points to pen) one, (points to pen) two, so the number is three.
This corresponds more closely to how indexing works in computers, and matches up nicely with the so-called von Neumann construction in mathematics, but in other ways I find it less natural than #1. But I am confident that you could teach it to children, and they would find it natural, and think it weird to mix up "the number of objects" with "the number of the last object". In this case, the only thing that changes from your dialogue is that Timmy says "Well, since the next number is three, it totally makes sense to announce that I have three pens." You count the pens, then you say how many there are. Zero, one, two, three. Not zero, one, two, two as you would prefer. What are you, some kind of weirdo or something? :-)
Here are two processes Timmy could use to count the pens on his desk. (I have numbered them starting with 1, because I considerately adapt to the needs of my audience :-).)
1. Say "0". Then increment for each object. So he goes: zero, (points to pen) one, (points to pen) two, (points to pen) three.
The advantage of this is that you don't need a special case when the number of pens turns out to be zero. Hey, Timmy, how many unicorns on your desk? Timmy starts by saying "zero", looks around, no unicorns, finished: it's the same process as for pens, it just stopped earlier.
2. Number the objects from 0, and then the count is the next number after the ones you listed. So he goes: (points to pen) zero, (points to pen) one, (points to pen) two, so the number is three.
This corresponds more closely to how indexing works in computers, and matches up nicely with the so-called von Neumann construction in mathematics, but in other ways I find it less natural than #1. But I am confident that you could teach it to children, and they would find it natural, and think it weird to mix up "the number of objects" with "the number of the last object". In this case, the only thing that changes from your dialogue is that Timmy says "Well, since the next number is three, it totally makes sense to announce that I have three pens." You count the pens, then you say how many there are. Zero, one, two, three. Not zero, one, two, two as you would prefer. What are you, some kind of weirdo or something? :-)