Yeah not many games have options like this. Another I like to play with and use as an example is the Summon Night Swordcraft Story (not sure if 3 has such things offhand but given it is present in earlier efforts I would not be surprised).
With that said the GBA palette is mathematically generated (mostly BGR) and readily changed in software. http://problemkaputt.de/gbatek.htm#lcdcolorpalettes
To that end I imagine you could do some kind of game wide* channel level colour correction or wholesale levels adjustment by sticking something to rewrite everything** in a vblank or other interrupt (done in an automated fashion for many things ranging from the cheat injectors like GBAATM and GABSharky as well as soft rest things like BOMA).
*might even be able to add some basic logic to check if a given colour is there and then not touch that palette.
**plenty of games already do palette animations. I tend to suggest the rainbow blocks in mr driller 2 as a pretty clear cut example, though the summon night games also provide a nice example with their save swords.
Suggesting this likely means I am hitting new lows and am way beyond even my usual "bodge it and scarper" approach but as far as technically feasible goes I would say it is, and only the rather limited (and usually fairly full already) processing window of the first choice interrupts ( http://www.coranac.com/tonc/text/video.htm
) and likely fairly intense processing required (not like the GBA has much in the way of matrix maths or SIMD support) to effect a palette wide change, especially if you have some kind of bitwise maths necessary, gives me any pause.
Conventional palette editing ( https://www.romhacking.net/documents/331/
for a basic introduction) is still by far a better method to employ but as the question was asked...