What gave you that idea? The game's palette was intentionally altered from the SNES original to accommodate the GBA's darker screen, an accommodation that is wholly unnecessary if you are using a DS Lite or a GBA SP 2.0. There are already similar hacks in the database for the Super Mario Advance games.
Well... previous games, like the SMA games you mentioned, is where I got that idea from. Now that you mention it, I do remember something about certain later model SP screens being better. But the original GBA was the core system. And games released on it specifically were design around the output color range of the system (or should have been, but there will always be incorrect PAR or color space conversions in developed games). And if that's drastically different from what is being seen on emulation, well... then there you go. There was also an issue with Gameboy Color systems vs GBA playing Gameboy Color (even some emulators have 'real colors' option for Gameboy Color). But now I can see it's more than just an emulation problem. So the answer to my question than is a simple; No, because there's a discrepancy between a range of GBA backwards compatible devices and even later parent/base model output differences. This patch fixes it for those devices.
In any event, considering that at least half of the colors remained unchanged, it is safe to assume that emulation accuracy is completely irrelevant to the subject at hand.
I think the only safe assumption from that information, is that they only thought certain parts or colors were relevant and worth changing... which implies a certain level of laziness on their part
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