Figured out now, I was missing the Atmega128_via_FTDI in the BOARDS.txt file. Both are needed below:
##############################################################
atmega128A.name=Custom ATmega 128 Breakout Board using AVRISP
atmega128A.upload.using=avrispmkii
atmega128A.upload.maximum_size=126976
atmega128A.bootloader.low_fuses=0xFF
atmega128A.bootloader.high_fuses=0xCA
atmega128A.bootloader.extended_fuses=0xFF
atmega128A.bootloader.path=atmega
atmega128A.bootloader.file=ATmegaBOOT_168_atmega128.hex
atmega128A.bootloader.unlock_bits=0x3F
atmega128A.bootloader.lock_bits=0x0F
atmega128A.build.mcu=atmega128
atmega128A.build.f_cpu=16000000L
atmega128A.build.core=arduino
atmega128A.build.variant=standard
##############################################################
atmega128B.name=Custom ATmega 128 Breakout Board using FTDI
atmega128B.upload.protocol=arduino
atmega128B.upload.speed=57600
atmega128B.upload.maximum_size=126976
atmega128B.bootloader.low_fuses=0xFF
atmega128B.bootloader.high_fuses=0xCA
atmega128B.bootloader.extended_fuses=0xFF
atmega128B.bootloader.path=atmega
atmega128B.bootloader.file=ATmegaBOOT_168_atmega128.hex
atmega128B.bootloader.unlock_bits=0x3F
atmega128B.bootloader.lock_bits=0x0F
atmega128B.build.mcu=atmega128
atmega128B.build.f_cpu=16000000L
atmega128B.build.core=arduino
atmega128B.build.variant=standard
##############################################################