I am not sure about the answer to your question but I'll share some of my ideas for getting bikes around.
I have two ideas depending on how intrusive you want to be with your AV's hard covers.
Keep in mind, I have not tried these yet. I have ordered parts for idea#1 and I'll put up a post when I find out how it works.
#1 - Less Intrusive (No holes No change)
I already have a Yakima rack system with Q-towers (from my old car). I checked my local Yakima dealer and it looks like the Q-towers can be mounted to the hard covers using a modified Q Clip #34. I would have to bend the underlip of the clip to more of a 90 degree bend so that it would fit more snuggly under the hard cover. I am going to try this out when the parts arrive. I will mount my front crossbar and tower set up on cover #1 and the rear one on cover #3. I am also thinking of cutting the crossbars to 50" so it lines up with the covers (i might be able to get my 48" to work, otherwise, I'll have to buy 58" and cut them), this should still allow for the side compartments to open. I can then put my four steelhead bike trays up there, my snowboard rack in the winter, or any other application my crazy mind comes up with. My preliminary tests have shown this should work fantastic. It will not affect the watermanagment system for the AV's bed in anyway.
#2 More Intrusive (Two holes drilled into cover #1)
Saris Traps Triple Track 47"
http://www.sarisracks.com/start.htm
mounted on cover #1. Triple Track has rubber sides and bottom and should mount very easily (it already has holes for mounting). Then the four bikes, staggered, could ride right on top of the hard covers. it would be just a matter of running a tie down between the two rear grab handles on the AV through the rear wheels of the bikes. This mod would be the easiest as far as taking the hard covers on and off.
Depending on the Yakima configuration (idea #1) you might have to remove the rack system before you removed the hard covers. If you have any yakima accessory that connects both crossbars together then you would have to unconnect them or you'll have covers #1 and #3 hooked together. But if you didn't, or had something like the snowboard carrier then you could remove each hard cover with the crossbars still attached.
Hopefully, I didn't make this too confusing. I should get the clips in a few days then I'll try it out and post some pictures.