How come some of the songs in the game are covers?
There’s a variety of factors. First and foremost would be technological. For a master recording to be suitable for the game, there needs to be a seperate guitar, bass, and vocals tracks as well as seperate tracks for each percussion instrument used for the drums. Some songs only have 4-track masters due to money/technological reasons (older bands are more likely to need covers than current ones), some suffer from tracks bleeding into each other (“Ten Speed” is cover, even though “Welcome Home” is a master, because the two guitar tracks bled into each other), some are in poor quality or just plain missing (I’ve read that Rush falls into one of those two). This thread has a good discussion on the whole process from licensing to market.