The face of the cd player I use flips down and the slot is near the top. I have not had any clearance issues with the shifter being the way. I am not positive about other brands or models. Like you said, there may be issues. But then that is where the stock cd player was placed too. It is both set back and at a slight angle down in the back. The only actual issue I have found is having to reach around the shifter in order to work some of the functions. Most of the time though I can just extend my fingers and reach it though. I like not having to take my hand completely off the shifter to change radio stations or the volume.