excuse me, ChillyWilly, i am not understand why to start at 0x400000.
There's a "USB Transfer" mode to the Neo Myth: while the Neo Myth is plugged into the MD, you can turn on the USB controller and then send a file from the PC to run immediately. This file is written to 0, with a maximum size of 4MB. Once you've transferred the file from the PC, the Neo Myth menu then runs whatever was uploaded to 0 as if it were a MD rom. This has been in the menu since the very beginning. Here's the relevant code from the very first menu from Dr Neo.
CMP.B #$80,d0 ; START
BEQ RUN_X4
NOP
Jmp MENU
RUN_X4:
lea MAKE30(PC),a0 ;BBBB
JSR PRINTA
JSR wjoy
MOVE.W #$FFFF,D0
MOVE.W D0,USB_ON
RUN_X4A:
jsr rjoy
NOP
CMP.B #$20,d0 ; C
BEQ RUN_X5
NOP
NOP
NOP
NOP
JMP RUN_X4A
RUN_X5:
lea MAKE13(PC),a0 ;BBBB
JSR PRINTA
JSR wjoy
MOVE.W #$0000,D0
MOVE.W D0,USB_ON
NOP
NOP
NOP
NOP
NOP
NOP
MOVE.B #$00,MODE
;*******************************************************************************
MOVE.B #$0B,ROM_Z ;
MOVE.B #$00,RBK_H ; A24~A25
;*******************************************************************************
MOVE.B #$00,RBK_L
;*******************************************************************************
MOVE.B #$01,SR_Z; ; GBA SRAM SIZE
MOVE.B #$00,SR_B ; GBA SRAM BANK
;*******************************************************************************
MOVE.B #$06,RUN
;*******************************************************************************
JMP MD5
When you pressed START, it turns on the USB and waits for the user to press C. During this time, they use the LINK feature in the Windows app to write a file to location 0. Once done, they press C and the menu jumps to the MD routine with the rom offset set as 0 (RBK_L and RBK_H both set to 0).
So clearly, the flash from 0 to 0x3FFFFF needs to be reserved or the first time someone uses the Link feature they will overwrite one or more roms (think if they had SMS roms in the flash - they could overwrite DOZENS of roms).
So there's three options here that I see: one, reserve the flash from 0 to 0x3FFFFF and keep everything else as it is; two, change the link function to write to a different location than 0 and change the menu to match it; or three, remove the link feature from both the app and the menu.

EDIT: The simplest way I can think of to reserve the space is when you format the Neo Myth, immediately add one menu entry that has a name like "USB Link" that is marked as starting at 0 and being 4MB long.