You can use either but containers just provide more space on one tile. Just be sure to put the zone on the container and your settlers will put stuff in them.
I'll take a look at auto rotation to make sure it's work as intended. For now, you can use the rotate tool in the utility (U) menu to rotate them however you like.
Thanks for writing this up. Agree with everything you've said. The issues you've stated are definitely on my list. I appreciate that you took the time to write this all down. :)