Here is a response that I received from Engr. Aung, Director AIT Solutions. Sharing for everyone's knowledge.
"You can consider the podium, Tower 1 and Tower 2 to be three different "towers", using multiple towers option. T3 is podium (Foundation to 3rd floor), T1 and T2 are Tower 1 and 2, starting from 4th floor to roof.
However, it is suggested NOT to use ELF base shear from analysis if you have multiple towers in the model.
Normally, ELF base shear for each tower above the podium is calculated manually for scaling purpose only. To determine the base shear for scaling of two towers resting on a common podium, it is suggested to compute the design base shear of each tower above the podium (using weight of tower above podium) based on code-specified equations manually.
Then, scale the base shear of each tower above the podium in a 2-tower combined model in different response spectrum cases.
You will have two sets of response spectrum cases: RSX-T1 and RSY-T1; RSX-T2 and RSY-T2.
Use 2-tower combined model to design each tower with corresponding response spectrum cases.
For podium design, you may use the envelope of those cases.
For application of wind load in multiple towers, it is suggested to turn on "Allow multiple towers" in the Option menu and assign the diaphragm names separately for each tower.
If the story height of each story is different between two towers, it is suggested to crosscheck the wind base shear of each tower above the podium with manual calculated results.
It is okay to connect two towers on a common podium.
It is suggested to check the in-plane forces in podium diaphragm due to movement of towers under lateral loads.
If the seismic gap is allowed at the amenity podium floors and no constructability and maintenance issues, you can also provide the seismic gap and analyze the towers separately."