If it's really just the glaze and the hole doesn't go through the ceramic itself, technically that shouldn't be a problem – nothing will leak. But: it is a defect, and especially with a new toilet, I would consider whether I really want to install it that way.
On the one hand: warranty definitely applies here, and you have the right to a flawless product. On the other hand: if moisture gets in later (e.g., when wiping or through condensation), it can soak in over the years or cause limescale buildup – it doesn't have to, but it can. And visually it’s not so nice either.
If you don't mind and you need the part quickly, it will probably be okay. But if you still have some leeway: better to have it exchanged.