The graphics pack includes the raw files deliberately, as it changes some of them to display properly. It only includes the files it needs to make changes to. It does look like some of these raws are out of date and need to be updated, but it shouldn't remove any Mushroom Kingdom content - the only files it edits from ROTMK is creature_mw_ocean, since the Cheep Cheeps were showing up as meat instead of fish. It looks like it will, however, remove some of the new vanilla tools, like bookcases and quires, until I fix it.
However, if you manually removed the vanilla creatures and plants, you'll need to do so again after installing the graphics.
Speaking of Phoebus, I was thinking of replacing the Phoebus tiles and creatures still in the set with the graphics from my Rally Ho tileset. Since both this and Rally Ho are based primary off SNES graphics, they should probably look better together. However, before making this change, I'd like to know what people think of it.
Some of the tiles have different purposes, so it isn't an ideal comparison. I can mix and match if, for instance, people prefer the road/minetrack looking Phoebus tiles over the Axle looking Rally Ho tiles.
Current tiles are on the left, Rally Ho tiles are on the right.
Obviously the layout is different, but you should be able to tell which creature is which.
Current (Phoebus) tiles are on the left, Rally Ho tiles are on the right.