I’ve seen the image of her in the comic many times. The darkness is just for dramatic effect, she gets introduced the same way in the show, being covered in shadow for dramatic effect. There is no way the ponies could’ve missed her being an alicorn walking around in broad daylight and she specifically calls herself a unicorn.
The IDW team being different from the show team means nothing either, these people still have to keep things in the comics as consistent as they possibly can with the show, their in-universe explanation for the inconsistencies proves that they do care about maintaining continuity with the show.
Hasbro has rules for them too on what they can and can’t do. I strongly doubt Hasbro would’ve told the IDW team, “Yeah, you can make Opaline whatever tribe of pony you want, so long as it’s just in a flashback.”. With how much emphasis this show places on unity between the pony tribes, there is no way they would’ve allowed a continuity error like that.