Can someone tell me if it's been explained why Shard powers are somehow capable of beating literal magic, something they have no understanding of or connection to? An example being the so-called "all or nothing/annihilator" effects being able to overwhelm magical protections that should be out-of-context/running on separate physics and thus safe? Or is this a case of AU where magic actually exists in Worm and Shards are tapping into it? But if that's the case, how are they beating divine powers? Are the Entities actually gods and thus their Shards are divine as well? Or is it just a case of creating a vulnerability to something so the story won't be a complete stomp and still has some danger?
LordR has made, for the purposes of the Forge and it's abilities, Magic and parahuman powers equivalent. Meaning that Annihilator capes are effective against magic defences. There are many reasons for this change in regards to the local metaphysics but I personally believe that two are most prominent.
Firstly, without the equivalence, Joe's abilities to copy magic powers would be neutered, and there are a fair few other abilities like Arcane Craft which would serve no purpose, as would most of the Magitech constellation. The way I see it, the change was to ensure that as many perks had viable means of being expressed throughout the story without having them feel like dead weight.
Secondly, and this is more speculation on my part than anything else, it was to remove the "He Hoo, I cast barrier and win," button that most Magic vs Shard stories have. Let's face it, if Joe can block any attack thrown his way just by drinking a small bottle's worth of liquid, the story wouldn't be anywhere near as fun as it is.
That being said, not everything is in context for the Entities. For example, Psychic powers, Psi, Psionics, whatever you want to call them, are considered OCP for Entities. I believe Lord mentioned somewhere he was following some DnD interpretation of the concept with the whole "They're different" thing when looking between Psi and Magic. While Psi abilities might not always triumph over Magic abilities, they are unprecogable and most of them can be quite ridiculous.
Joe, currently, doesn't have conceptual based tech. Magic that say "user will be invulnerable, without any exceptions, for a (insert duration)" - I doubt Shards can break. But currently all his defenses have only almost unlimited capabilities (there's one alchemic trick that gave him invincibility against one attack, though). So, through that "almost" some annihilators can affect him.
As stated above, Shard like Sting can break the Alchemic Invincibility magic potion due to the Shard/Magic equivalency imposed by the Forge. Unless the effect is something like Fiat-backed indestructibility like the Minecraft perk provides with its indestructible armour, Sting will most likely be able to pierce it.