I could not find any way to directly specify the option for the project-based compilation. Instead, one must use the optoins set in the modelsim.ini.
Solution 1 (global):
update your system installation's version of the modelsim.ini to change the VHDL93 setting. This update would apply to all uses of the simulator.
Solution 2 (local):
Utilize a custom modelsim.ini file for the wizard and specify to use it in the project new command. Here's an example of modifying the wizard compilation commands:
Here is the contents of the ini file:
And here is a snippet of the resulting vcom compilation commands:
