It's goodwill. In your servicing and warranty booklet, it's stated explicitly that the warranty does not cover rattles. So any repairs that are carried out by your dealer with regards to rattles are not reimbursed by Honda Australia.
I went through my booklets and I can't find where it said, so eventhough I remember reading it somewhere. Well, for now I retract my statement until I can find where I read that rattles were not covered.
BTW, my friend's Civic Sport doesn't have the rattles that you describe, hasn't lost any trim parts and the driver door closes fine. If you have a lemon, then it is not representative that the made in Thailand Civic is inferior in quality (build quality and quality control). You need high number of failures across a large number of owners before you the model will be considered by HA to have a legitimate problem. Even the very common engine block problems in the SS blocks in the VX gen was not acknowledged by Holden as a legitimate defect.
Bookmarks