ino.hex vs ino.with_bootloader.hex
If flashing with AVR In System Programing (ISP) the bootloader is not needed. Only the flashing over Serial needs a bootloader. 

The ISP erases the flash including the bootloader. To be able to use the serial flashing after ISP, the hex with_bootloader can be used. 

I flash AVR over WiFi with esp8266's core AVRISP library and I use the hex with_bootloader to have the option of flashing later over USB.

Your Android app will use the serial flashing utilizing the bootloader. The bootloader doesn't delete itself. So you should use the hex WITHOUT bootloader.