Before kids and car seats I would put the bikes inside for security and gas mileage. I made this mount using an aluminum threshold from Home Depot, some bike tites and Yakima wheel forks. This was a solid setup for road and mountain bikes but required removal of the seat post.
I ran a Yakima roof rack for many years with up to 4 Yakima Steelhead mounts. It was a strong and stable setup. I travel a lot with bikes and I didn't like opening my bike up to possible damage on the roof, stone chips and decreased gas mileage. I also didn't like the idea of forgetting bikes are up there as well as getting the 4Runner all dirty with a muddy bike.
The bike saying, "Don't forget I'm up here."
This bike saying, "Dude, you forgot I was up here." Wife driving, her bike, her rack, her car, my repair.
With all the driving I do with bikes I decided to take them off the roof. I like the Yakima fork mount racks and wanted to keep them. I bought a Thule hitch mount bike rack off of Craigslist and cut it up, welded some metal to it and then installed the Yakima Steelheads to it. It's set up to hold 2 of any of my wife and/or my bikes without touching each other or the vehicle. It's solid, secure, tilts down for rear hatch access and is high off the ground. This is good because I can see them through the back window and they are far from damage if I take everything off road.
The bike closest to the 4Runner has narrow bars so it's spaced back. The tray is placed so that there is a couple inches of clearance even with my widest bared bike.