There's obviously some inconsistency going on here in the app approval process, but the main gist from Apple has always been the same; they don't want users getting confused about whether or not they are chatting it up on Chess Wars or via SMS.
My company was told something similar by Apple reps at an iPhoneDevCamp event: make sure the chat bubbles look different so as not to be confused with our native app.
They can request you don't use it as condition for access to their platform - claiming it's a trademark is different. The mark (in the EC at least) needs to be indicative of the origin of goods or services and needs to be distinctive in order to achieve that aim - chat bubbles are not distinctive and are not indicative that Apple Computers Inc. are providing the service. Fail IMO.
My company was told something similar by Apple reps at an iPhoneDevCamp event: make sure the chat bubbles look different so as not to be confused with our native app.