Technically, you are correct. The Apple pencil 2 has a diameter of 8.9 mm, whereas an AAA battery has a width of 10.5 mm. So, Modifying the Apple pencil to use a regular AAA battery would MAYBE add 2-3 millimeters to the Apple Pencil.
I personally think it's not that much, but...
SUPPOSE you REALLY want a slimmer pen. Instead of using an AAA battery, you could use 1-2 AAAA batteries, which have instead 8.3mm. So, it's a bit smaller than the Apple Pencil.
I think just one rechargeable AAAA battery would do, because the internal battery of the Apple is around the size of an AAAA battery (maybe slightly longer, even):
If a Microsoft surface pen can last 15 hours per charge (double the charge of the Apple pencil, 7-8 hours), I don't see why Apple wouldn't be able to pull this.