Generate and flash a binary file for STM32
That depends on your bootloader application. Can it read HEX files?  
You use the target dialog in the target options, or a scatter loading file.  
You do not include empty regions this in the image. Keil includes a tool to create binary files.


Note that you might want to sign your binary file with a checksum. The arm linker cannot do this. But you can do this with SRecord. (also removing/converting regions)