Love my bakflip. Never had a problem with riding with it open for an extended period. We drove from Louisville to Destin FL last summer pulling that camper and with bikes in the back of the truck. I just flip it all the way up and use the bars to secure it. I have it settle in going down the road and one of the support bars disengage. Since I now know that, I make sure to get it in a position where it shouldn't move but still check it when we stop.
I did figure out not to drive with it just partially flipped (not while pulling the camper). I tried that when having something else in the bed of the truck and not needing it all the way open and then wind got it and flipped it closed.
It's not a gentle flip doing that either. Got a few dings where it hit my cargo but it's on the inside so all is good.
As you can see from my picture I opted to push the bikes tight together and out to the side to gain some storage space in the middle. I offset the mounts so I could do that without the handle bars causing a problem. I saw where others put the mounts on at an angle to help with the handle bars but I didn't like how the bikes wanted to lean that way. I would think you could put all 3 bikes tight to one side and still have enough space for your tote n stor. You might even be able to turn it on the side and strap it to the side of the bed since you have to have the cover up anyway. I don't have one so don't know this for certain.