I am also a fan of doing this. However, I prefer to add rather than replace or subtract. So if there is a beast similar to a displacer beast with a scorpion stinger, for example, just let the PCs wonder ‘what the hell did we just fight’, rather than saying that these are displacer beasts and replacing them.
The place of mind flayers in DS is in the context of an adventure instead of a supplement. That way the mind flayers only happen in DS if the PCs actually participate in the adventure. See Expedition to the Barrier Peaks for something similar. Are there really robots in Greyhawk? Most say no, but there are PCs in some groups that have fought robots and won.
I’m not huge on mind flayers on Athas. I’ve seen various ideas about mind flayers and most of them position mind flayers deep in Athas’ historical narrative. My approach is minimalist. It’s saying “here, if you want mind flayers in your DS campaign, here’s how you can do it without warping the setting”.
Keeping the setting intact and following broadly the Dark Sun themes is my MO.