The ‘improved’ versions sound muffled like I have water in my ears. Plus I’d rather hear the game as it was designed, artefacts and all.

The artifacts weren't a conscious design decision, they were a constraint. We don't know whether the designers would have chosen to keep them or not, if they had the choice.

GBA games were made for a console that behaved like this.

Accuracy is paramount. Targeting else than the console's sound is an affront to preservation.

Preservation and design intent are two very different things.

The idea that sound designers on old games were totally siloed and ignorant of how their compositions would sound on final consumer hardware is completely wrong. Most of these composers were programmers themselves and knew exactly how to get the final hardware to make the sounds they wanted, even when they composed using more advanced tech.

Programmers using devkits (more powerful than the consumer hardware) likewise.

I don't understand what you mean. Nobody said they didn't know how their compositions would sound, my argument is that at least some of these composers would have chosen the more advanced interpolation method, if it were available.