You can sand the top of the LED. As long as you don't go down to the metal parts it will still work, just the focus of the lens will be affected, but it's not important with this type of backlighting.
The jelly POM set is the only place I know of to get a white or pink POM spacebar... I can send you an OEM profile white PBT spacebar if you like, but it's quite pure white, not soft white like the jelly POM one.