According to the warranty, this is what you are entitled to:
If during the Warranty Period you submit a claim to Apple or an AASP in accordance with this warranty, Apple will, at its option:
(i) repair the Apple Product using new or previously used Apple genuine parts that have been tested and passed Apple functional requirements,
(ii) replace the Apple Product with a replacement product of the same model (or with your consent a product that has the same or substantially similar features as the original product – e.g., a different model with the same features, or the same model in a different color) that is new or comprised of new and/or previously used Apple genuine parts and has been tested and passed Apple functional requirements.
The “slightly bent” statement concerns me. Will the pencil still charge? Is it functional? You may want to contact the warranty department again and question the condition of the replacement.