As far as I know, the only way to achieve that is to use a program like Cheat Engine to alter the active memory addresses for clothing. It's the only way I know of to make Kotone wear a shirt without a bra, since I know of no way in the game itself to remove a specific item of clothing.
The save file may have values that correspond to the individual pieces of clothing, but after some experimentation, there are either no such values, or they're currently not being used to record specific clothing states.
The only clothing value in the save file that I can confirm does exist is for the specific outfit. If you were to open the file using NotePad++ or something similar, that value would be found on line 1013. A value of 0 is the default outfit, 1 is for Cool Breeze, 4 is for Sakura, and 11 is for the default outfit with a Green top. The lines immediately before it, for reference, govern Max HP (Line 1010), Attack Power (Line 1011), and Max MP (Line 1012).