I believe captain's chairs are only standard on the Signature trim. GT and lower have the option of captain's chairs or bench seat. When I go to the mazdausa.com builder, it lists (under trim options):
2nd-row 60/40 bench seat with power tilt-and-slide 3rd-row access
Then, after choosing your colour, it presents the free option for 2nd row captain's chairs.
It seems that your local dealers may just be getting GTs with the free captain's chairs option installed instead of the standard bench seat. Your dealer should be able to bring in a GT with the bench seat if they don't have any on their lot.
What did you end up replacing your previous CX-9 with?
We were able to get a GT with a bench seat in the color (white) we wanted. The dealer told us there were only 2 in their swap area and located one at another dealer 170 miles away. So it can be done.