I think you guys are going over board here.
As far as I am aware the only album that has problems with the mastering is Californication. I am not saying the other albums are high quality, but they are not much worse than 99% of the stuff out there. In fact, the vinyl version of Freaky Styley is one of the last vinyls I purchased that was on the thicker old vinyl before CD's took over and the industry started pressing vinyl on rolling paper.
As regards to the ops question; the "FLAC discography" you are referring to is someones rip or collection of FLAC rips from the original CD (or perhaps vinyl) source material. All modern recorded music (as far as I am aware of) is available in uncompressed format and can be compressed into a number of formats including mp3 from 320<--->20. The stuff you find on file sharing sites tends to be in the lower "lossy" quality formats which is higher compression for the purpose of sharing over the internet.