Yes, you can easily get Army Institute of Technology, Pune with 90+ percentage in 12th even if you are civilians through PMSSS .
I have lots of friends in AIT through PMSSS who are civilians. To get CSE or IT branch in AIT more then 91 % is required and with 98 you have a very good chances to get admission there.
The only things you have to take care is choice filling, many students do mistakes in choice filling and get a different college.
One suggestion i would say is though AIT is one of the best college in Pune, with 98 you have chances of getting DTU, COEP, Jadavpur and many other great colleges with good placements.