Why don't I have a custom title by now?!
If you look at the arachnotron sprites with SLADE 3 (which, contrarily to SLumpEd, definitely does not assume index 247 or any other in always transparent), and use a very contrasting background color, you'll see there are true transparent pixels.
Unless you're talking about another pixel, that is not a clear pixel, just the practice in many tools to color the background with index 247, which is shown as cyan in those tools but is black in DOOM and is used in various graphics.
Affected are BSPIA3A7, BSPIA4A6, BSPIA5D5, BSPIB1E1, BSPIB2B8, BSPIB4B6, BSPIC2C8, BSPIC3C7, BSPID3D7, BSPID4D6, BSPIE2E8, BSPIF2F8, BSPIF3F7, BSPIG4G6, BSPIH1, BSPIH4H6, BSPII6, and BSPII7.
It's also quite explicitly used as the transparent color in some of the Doom alpha picture formats.
In the DOOM IWADs, index 255 (RGB 167/107/107) isn't used in graphics and unlike cyan (which has nothing to do with DOOM internally), it isn't a glaring color and contrasts well with the images. I'm guessing they reserved the color as the background for editing when they made the game. Supporting this theory is that it's a unique color that isn't part of any range, and it's at the end of the palette.