Sadly, the D6 fuse setting is not fixing the issue.
A few things learned...
-The Rev2 board is indeed 16MHz (Rev 3 went to 10 and thus the gibberish board).
-Uploading the configurator sketch does indeed bork the memory the second time around.
-The setup is correct, outside of what happening to the memory on each programmer based upload.
Here's the output from console, does the 4294967295 number mean anything in particular? Strange considering all blocks get that same number written to them (sketch reads memory upon upload, then you press "w" and it writes a new serial number, then reboot via battery to check the serial sticks)...
Welcome to Configurator 1, compiled Apr 18 2018
Working with config protocol version: 2
Printing Device Configuration:
Protocol Version: 4294967295
Serial Number: 4294967295
Hardware Version: ⸮
Boot Counters: 4294967295
Event Counters: 4294967295
HTTPS Session Counters: 4294967295
Network Retry Counters: 4294967295
Session Fail Counters: 4294967295
w
Working with config protocol version: 2
Printing Device Configuration:
Protocol Version: 1
Serial Number: 3482810481
Hardware Version: 1
Boot Counters: 0
Event Counters: 0
HTTPS Session Counters: 0
Network Retry Counters: 0
Session Fail Counters: 0
Welcome to Configurator 1, compiled Apr 18 2018
Working with config protocol version: 2
Printing Device Configuration:
Protocol Version: 1
Serial Number: 3482810481
Hardware Version: 1
Boot Counters: 0
Event Counters: 0
HTTPS Session Counters: 0
Network Retry Counters: 0
Session Fail Counters: 0
Here's the setup for the boards.txt file as well...
##############################################################
MoteinoMEGA.name=MoteinoMEGA
MoteinoMEGA.upload.tool=arduino:avrdude
MoteinoMEGA.upload.maximum_size=130048
MoteinoMEGA.upload.maximum_data_size=16384
MoteinoMEGA.upload.speed=115200
MoteinoMEGA.upload.protocol=arduino
# This line added
MoteinoMEGA.bootloader.tool=arduino:avrdude
MoteinoMEGA.bootloader.low_fuses=0xDE
MoteinoMEGA.bootloader.high_fuses=0xD6
MoteinoMEGA.bootloader.extended_fuses=0xFD
#MoteinoMEGA.bootloader.extended_fuses=0x05 Didn't need this!
MoteinoMEGA.bootloader.unlock_bits=0x3F
#MoteinoMEGA.bootloader.lock_bits=0xCF Programmer expects 0x0F
MoteinoMEGA.bootloader.lock_bits=0x0F
MoteinoMEGA.bootloader.file=DualOptiboot_V5.0_atmega1284p_BlinkD15.hex
MoteinoMEGA.build.mcu=atmega1284p
MoteinoMEGA.build.f_cpu=16000000L
#MoteinoMEGA.build.f_cpu=10000000L
MoteinoMEGA.build.core=arduino:arduino
MoteinoMEGA.build.variant=MoteinoMEGA
MoteinoMEGA.build.board=AVR_MOTEINOMEGA
##############################################################
We're so close!