You first have to beat the final boss. The code for the organic machine is at the end of the credits. The organic machine only does 2 things
1. fixes the shit ass fonts citizens of the expanse use
2. if activated at the start of the game, gives an early Glutton Emblem and EXP Scarab. As far as I'm aware, this is the only way to get all 4 EXP Scarabs.
Grinding is not necessary, but you will often have to fight a huge number of enemies while trying to unlock various secrets. Fights can drag on for a long time, especially on nightmare difficulty. Beating the game and all post-game content took me 34 hours! It would be nice if enemy spawns were halved and enemy rewards were doubled. A lot of the game is spent doing the same fights over and over.