2. Assuming that FDTI overwrites the bootloader, can I then at some future time reinstall the bootloader using the USBasp device?
3. About how much EEPROM does the bootloader deduct from the program space?
This sounds a little confusing to me. The FTDI chips on the Arduino boards, as well as
the FTDI Cables and FTDI Friends that some of us use, in lieu of having the FTDI chip
on the board, do NOT overwrite the bootloader. They use the bootloader to install
the sketch in Flash.
Also, I believe the bootloader resides in Flash, not EEPROM.