The underside of the cover is simply being oxidized and bleached out, as it lives over a hot, chemically treated environment. Excessive chemicals can damage your cover prematurely, but normal chemical use will cause the underside to lighten up or bleach out. There is no detrimental effect unless you are on the excessive side of chemical use and the underside can and will "blister", "waffel", or otherwise deteriorate.
All covers will eventually be replaced in time and you may consider the cost of a cover to be $100 a year. The better the cover is made, the longer life you get from it, and the more you pay for it.
You are noticing something that is naturally going to occur to all covers, just be sure you are not on the excessive side of chemical use.