Warhammer 40k: I'd tier them very differently. I'd distinguish "material" from "immaterial" damage, as in, damage from purely material sources (technological, biological...) V.S. immaterial sources (psychic & Warp-based) would be resisted differently depending on the being, and mingling of both sources would be a case by case analysis (A planet that exploded as consequence of supernatural influence and telekinesis being used to smack a mundane object against someone would have influence from both, so both would contribute, in different ratings and inconsistently, at survival). Primarchs would probably be 4-B against immaterial/supernatural attacks, tier 7/6 somewhere-ish against purely physical threats, and most characters would have serious revisions from this. In particular, Macharius should urgently be downgraded to Astartes tier, and that is being generous. The Emperor is a bit of a special case and would require further analysis. In fact, on the off chance I someday stop being lazy, I will spend a few days collecting scans and wording a good argument for that. As it is in the wiki, I feel 40k is misleading.
Baki: God-tiers should straight up be Low 7-B-ish, but the current arguments make a lot of sense, so it is very fair for them to be lower.
Darkest Dungeon: 9-B to 9-A at most, even at endgame. Speed is also very wrong, they should be Subsonic to Transonic-ish.
Shinza Bansho: 1-A Gods, at least if the translations I've seen from Kajiri Kamui Kagura are correct. I was going to say that the Ewigkeit users always felt 7-B-ish rather than 7-A but that's changed now, so I'm fine with that. The low-tiers in Dies Irae (like Human Wilhelm, Machina and Schreiber) should be 9-B with Subsonic speed, combat and reactions, unless the manga isn't canon.
There are more things but those examples jump to my mind.
I'd also personally change how people treat calculations, "bullet dodging" in fictional series and things like HP mechanics, but that's a more general thing. Since it would affect a lot of verses, I included it here.