Some of the A/T 75mm motors will run in CTI cases, and while I have no first-hand knowledge, I understand that some of the CTI reloads are certified for Aerotech cases.
When I bought 75mm cases, I went with CTI 6XL-grain and 4-grain cases, the closure hardware, and two spacers that would let me run any size CTI motor from 2 to 7 grains. (The 6XL is actually a full size grain). This ended up being less expensive than getting the A/T 5-grain starter kit and having to purchase the 6-grain case separately. And still not having a 7-grain option.
By going with CTI I could run 2 through 7 grain motors, for less money that going with A/T hardware and being able to run 1 through 6-grain motors (with two spacers for each system).
What I didn't know at the time was that not all A/T 75mm motors will work in the CTI cases. Specifically, some of the A/T nozzles won't work with the CTI rear closure. I think it might be their "Medusa" nozzles (someone check me on this if they know). I found this out when I showed at Black Rock with my CTI 7-grain case and bought the A/T M685 6-grain long-burn motor for a special project I had built (75mm minimum diameter carbon fiber missile that I wanted to sent to the moon
) Got back to the table and realized that it wouldn't work, so I ended up buying 6-grain A/T motor hardware on-site. Because I was not going home empty handed. But I did go home empty wallet-ed.
At the end of the day -- no right or wrong answer. You have to look at what motors you want to fly, what brands your local vendors carry or you can buy on-site, what size rockets you'll be flying, etc. I'm am fortunate to be able to go to Black Rock once or twice a year, and when "the sky is the limit" (which it is out there) I wanted that 7 grain option, and that more than anything drove my selection of the CTI cases.