What does transparent mean here?

Transparent as a system/box can be, meaning that you can't see / know about it. (Yeah, I guess you can read that not transparent as obscure in disclosure of how their system works, but it shouldn't make much sense)

AWS is super clear what resources are zonal and provides tons of guidance around making things multi-AZ.

Yeah, they allow people cheaping out for zonal resources and then going down with their zone.