Certainly pros and cons to each type of mount. The best situation for most cyclists is to be able to stand a bike upright inside the vehicle for a few different reasons, but with the CX-5 that is not possible. If one doesn't mind using a cargo cover/blanket and laying it down with the seats down that is not a bad option, but eventually something plastic or painted is going to get scarred the more loading and unloading. I ended up with a White/sand interior CX-5 and I am absolutely nervous now about transferring grease from one of my bikes to the upholstery. One of my next purchases will most likely be getting Wet Okole black seat covers since I usually end up soaking in sweat and never fails I have spot of grease on my leg or somewhere.
With my last vehicle (Nissan Titan) I could stand the bike upright (front wheel off) behind the seat and feel more at ease leaving the bike unattended when going in a store or to eat. Not boasting, but each of my bikes are valued over $5K so it is something of a concern. I have a lot of friends that drive Honda Fits or SUV's that allow their expensive bikes to stood upright inside for security more so than for gas usage and still have some cargo room for gear bags and coolers.
I am an avid cyclist so my loading/unloading rate will be far higher than most people. It never fails that grease from the drive train or the fork gets hung on something or the day you finish a ride totally exhausted and you accidently scrape the bumper with the bike while loading seems to happen. I know that I get sloppy after a hot 100 mile ride and the car will show the impact of me being tired. I do like some of those cargo blankets shown on this forum that has an extension that drops out to protect the back of the car. That really looks nice.
I did not go with a roof rack because it does catch more air, debris and bugs, but also because I am short and would need a ladder to get the bike mounted up there.
I went with a wheel tray type of rack that I felt I could add cable locks a bit more easily and where the bike is more stable without swaying or adding more bungie cords to keep the front wheel from moving.
Whatever you guys choose there are a lot of good options. I just hope you enjoy the activity of cycling or other form of outdoor fitness.