Good to know it wasn't just user error on my part.It's the latter. Redshift code runs once before that section of memory is completely unmapped and mapped to the DS/GBA side.
The more surprising thing is that it doesn't crash when waking up from sleep mode, as sleep mode always crashes for me...
I will note after some playing around I think I have discovered at least a workaround for this, however, since my 3DS is almost always on charge when I'm not using it, I can't validate its effectiveness as far as battery goes.
Basically, before closing the lid/putting the game in sleep mode I have been using the Select + Down + L shortcut to open the .nds/ROM menu and leaving it on-screen and the game suspended. It seems that as long as this menu is open, when I return to the game later it will retain my Redshift adjustments and I can simply close the menu and continue playing.
Again, I can't speak for the effectiveness of this workaround where battery is concerned since I'm not sure if this puts it into actual sleep mode or just turns off the backlight the same way it does when you close the screen running the built-in GBA VC.