I agree with you. The 3 year manufacturer's warranty is more comprehensive than the 'used' Relax warranty and doesn't have the exclusion for trim. I would therefore insist this is fixed under warranty unless they can prove it was caused by neglect.
As for the leather, it's a common complain, especially for perforated leather, and Lexus seem to put it down to wear and tear and a character of the natural material. I don't think it's bad enough to take it to court for not being fit for purpose.