I thing the snug fit has alot to do with how the installers does the work.. I mean sure the covers can be huge and not fit but a install who has done them before can adjust and make them work without taking away from the seats look factory. I had my interiors pieces professionally painted but there is many paints that will work for your lids. What is rubbing off on them is the thin layer of rubber for protection so that they don't get scratch or whatever. I would sand them down and get a good spray paint and then a good clear coat spray. I have used a paint which you can get in Home depot. The lids are as well as every trim piece is overpriced in the boxster so... I would even go as to get them professionally painted before opting to buy news ones.. as it bound to happen again.
http://www.homedepot.com/h_d1/N-5yc1vZ1xgf/R-100670334/h_d2/ProductDisplay?langId=-1&storeId=10051&catalogId=10053i