The other potential option might be to upscale the GSC tileset, then scale it back down to the required size for the GBA games.
Not a perfect solution and might need some tweaking...
Perhaps look at either ESRGAN and the many models released to mass/bulk scale up the tileset. Then run a script to scale back down again.
Otherwise I think it was scalenx that produced rather clean results for upscaling (filter seen in retroarch) of pixelart. Using that as an upscaler, then nearest neighbour or bilinear filtering down again with a limited palette might be the way to go?