When we told Pak Rustam, our guide cum driver, we wanted to buy t-shirts to bring home, he took us to this one shop named "Jogya T-Shirt". There were not only a wide range of shirts to buy, but there were also other kinds of merchandise such as batik products.
There was a waiting area (most probably) for men while the women were busy shopping and queuing up at the counter. There was also free mineral water.
The biggest t-shirt in Indonesia for customers to see.
No doubt you could buy cheaper shirts in a more touristy place like Malioboro Street. Nevertheless, I think this place sold better quality and more reliable t-shirts with the exact sizes you wanted. I had had some bad experiences getting S-sized shirts even though the labels were clearly printed with XL.