Quests and "Instant Mine"
My "Instant Mine Node" popped and my quest did not track the full amount, why?
So first we must explain the way skills/enchantments work. There really is no ability to do "magic" stuff in Rust. The plugin uses trickery to make things seem like new abilities and features. But it is all smoke and mirrors. And the quests just use simple Rust hooks to track things you do in the game. For example every time you smack a node your game calls "OnGather" hook which is how Rust knows you just got X amount of stone. The quests plugin monitors those hook calls and if it see OnGather it just reads the amount that Rust is communicating that you gathered and then adding that to your quest progress. This is also why it only counts vanilla gather rates because the gather bonuses are not actually making you "OnGather" more stone or metal ore, they are simply watching that same hook and then 'admin.give' the extra bonus amount to you. More smoke and mirrors.
So back to Instant Mine.... When you hit a node the plugin rolls the dice and if you win the dice roll on "Instant Mine Node", it performs more smoke and mirrors. It first identifies how much stone is left on the node. It then does the admin 'entity.kill' to make the node vanish. And then it 'admin.give' you the remaining stone it identified. So notice no "OnGather" hook is called there. It deletes the node and then just sticks the remaining resources into your inventory to give the illusion you "completed the node".
This is why instant completion of the node seems to be skipping some quest progress. The quests cannot see that last bit of resources because it is never called on by the "OnGather" hook.