PSA: Atlas mechanics are capped!

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Every map can contain a limited number of mechanics. Mechanics include things like Master spawns (Einhar, Alva, Niko), Archnemesis, Harvest, Delirium mirrors, Strongboxes, Shrines, Harbingers, Heist caches, etc. This cap is map specific and not visible to the player. Once a map reaches its mechanic limit it cannot spawn additional mechanics.

For example: You run a Dunes map. You select Harbingers from Kirac. You place a legion scarab, an ambush scarab, and a expedition scarab into the map device. You have spec'd into Harvest chance and Deli chance on your atlas. In this example you've surpassed the amount of mechanics a Dunes map is capable of supporting. There is a 0% chance of a master randomly spawning. Your deli and harvest Atlas points are wasted. They cannot spawn.

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It's not a cap. It's a tileset limitation that has always existed. You were losing mobs this whole time if you were trying to pack Dungeons or Cells. If the game can't find anywhere to put the things, it will simply cull them.