A couple of obscure variations I have. I’m not sure if you’ll see find these worthy of being indexed…
First, with Amazing Spider-Man 320, the main direct edition has Paladin in the barcode box. However, there is an edition with Spider-Man’s head in that box. The ONLY copies I am aware of with Spider-Man’s head were originally available in the UK. I wonder if there was some UK multi-pack that has those
Next, there are two nearly identical editions to the DIRECT edition of Amazing Spider-Man 387. But the variation happens with the back cover.
Some direct editions of ASM 387 have a Spider-Man and X-Men video game ad. Some direct editions have an X-Men trading cards ad. I have only ever seen a newsstand edition with the video game.
Spider-Man and X-Men video game ad (for one of the direct editions and the only version of the newsstand edition I have seen):
X-Men trading cards ad (for the other direct edition – I have never seen a newsstand edition with this back cover)
I happen to find an eBay listing for both versions. CGC doesn’t make any indication.