According to both the relevant Grimoire card, such as Ishtar Sink, and the Advisors tab of the Legend page, reaching Kill Rank 2 on a planet is supposed to enable the Resource Income Bonus and cause "Extra materials drop from material nodes in this destination" which I take to mean you should receive at least two materials when you collect from a node. I have unlocked this for Venus, but it does not appear to work as I still only receive one Spirit Bloom when harvesting. I intend to receive a fair portion of my marks by turning in stacks of materials, and increasing the rate at which they can be collected make a difference.
I have also unlocked the Glimmer Income Bonus for Dregs, which causes "All characters earn more Glimmer when this combatant is killed with a Glimmer-drop consumable active" but I have not tested it yet.
I would like to know if these bonuses that can only be found here on Bungie.net are active in game?
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Have you looked at the Grimoire card and actually activated the upgrade? like on weapons and armour? Took me a while to figure out