I wish I could be more helpful on crates. I have put three cat carriers in the back on the way to a rescue at times. Getting one large crate in the back would be an accomplishment. The best idea I can think of is customizing a pair of wire cages. Another idea if it's just short trips is unlatch the hatchback, but secure it with rope.
Maybe removing the passenger seat and putting one up there and one in the rear would work better? That would at least leave more room for each of them. When I have to put my dog in the car I put her in the rear and have gotten her trained to stay sitting down. Usually she moves forward and hangs her front paws off of the wall behind the seats and is comfortable from there. She requires no crate so I guess I can't really help on that account.
Those are big dogs. We are currently driving cross-country and have small bird cages in the back, here is photo 1 and photo 2. The cages are about 12"x12"x18" and leave about 3" of space that I can see over them out the back hatch.
I've never done crates, but my girl (all 90 pounds or so of her), is quite happy riding in the back. I think she thinks of it as her little den
Do you need the crates to keep them separated, or just for general restraints? For the latter, I think I'd start with one of those net "tailgates" you see on pickups, cut it to size, and figure how to mount a couple of anchor loops near the upper shoulder belt mount point. Then use some 'biners to snap the net to them. For separation, you could run a second piece down the middle...
I can fit two Golden retrievers in the rear. They are really good about staying behind the bulkhead.
I really like the net behind the seats idea. It is easy to remove the seatbelt anchors on the "B" pillar to attach a clip there. Then you could attach the lower portion of the net to the loops on the bulkhead.
I don't really have any ideas on the crate thing though, except DO NOT drive with your rear hatch open. The inversion current from the back of the car will suck the exhaust fumes into the passenger compartment. This is very bad. (you can get carbonmonixide poisoning) You might be able to get away with it in the summer with all of your windows down and the AC at full blast, but otherwise don't do it.
I have had 300 lbs of lead acid batteries on the top of the rear deck, so I would not worry about the weight.
If the dog decided to have a leak, I would worry about the electronics that are under the cover, so it may be prudent to put down a waterproof cover.
Wow you guys have thought of everything. I was wondering about taking my Doberman for a ride (he's 1.5 years old, only about 68 pounds right now). The main thing I was worried about was having him fly into the front of the car and/or get tossed around in the event of an accident. I suppose the best idea would be to put a harness on him and tie him down with bungees or something... using the hooks that the cargo net is supposed to utilize. I wonder if those are strong enough, though...