Ok, I've figured out the problem. This only happens when using a sprite sheet in a collection. Once you have sliced the texture and are in edit mode, if you have two different materials (one solid, one transparent) being used in the sprite collection, then once in the Tilemap Editor, it will render the tiles in the palette as if they all have a solid material. This only affects the palette, and once you place the tile, it renders correctly. The palette renders correctly if you only have one transparent material being used.
So you can check this out for yourself:
-Make a new sprite collection
-Add a sprite sheet that has some transparent tiles
-Slice, apply the config settings
-In the settings, use the default material which uses a transparent shader
-Use the collection in a tilemap editor and notice the palette should be rendering the tiles transparencies correctly
-Go back to the sprite collection and add a new material, making it solid
-Change one of the tiles to use the solid material
-Commit changes, go back to the tilemap editor, now all the tiles in the palette are rendered as solid