1) If I upload may application .hex file to the chip with the programmer via the ICSP connector & AvrDude, this will overwrite the bootloader.
I could be forgetful, it's been a while sense I've done anything other then just burn the bootloader into a chip, but I don't think #1 statement is correct.
The bootloader lives in high flash memory and is protected from being erased by the fuse settings in the chip. I believe you can just burn your .hex file via USBtiny ICSP and not disturb the bootloader. But either way It does sound like you can do what you want even if it takes a second step later to erase the chip and reburn the bootloader.