Programming ATmega2560 processor with FTDI instead of ATmega32
In fact, the basic Arduino Mega (with the ATmega 1280) utilizes an FT232RL, so yes, it will work if you connect it correctly.

It is only the newer Mega2560 (along with the similar-generation Uno, etc) which utilizes an ATmega16u2 or similar as the USB bridge.

Generally speaking, the bootloader doesn't care - you should be able to use either target chip with either USB bridge (or others).