Our pup loves his spot on top of the Alpha system. I think it's just a factor of being high enough to see out while laying down. In other cars he seems to get a bit car sick, but loves riding in the 200. Whatever you do, putting them on top of the system is a good idea. Also gives them more space side to side since you are above the wheel wells.
Crates don't fit well on top of the systems. If you get a system like the TB or the DIY above you don't really need a crate. I had a customer insist on a custom crate to fit his large pup on top of the system and it was ridiculously complex with all the angles. I'd say crate for small dogs is ok, for med or large dogs just get some type of divider system.
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