I have replayed from a clean safe a couple of times and the problem does not seem to appear, my guess is that in-between updates and your save file something might have untriggered the condition required to have the crafting option, this could happen in rare cases depending on when your save was created and what changes have been applied since. I have implemented a redundancy trigger upon defeating the Summoner slime again after the mission. This should allow you to fix the save file check by fighting the boss again. This change should be up and ready on the next patch. The game is pretty much still on Alpha and stuff like this could happen between updates, thank you for reporting it. In the meantime, if you wish to try out what the key unlocks before the next patch, you can start a new save. On the bottom right of the world map there's a blue tree that allows you to access the cheat room. There you can make up for a lot of lost progress if needed. If this is a specific version bug, and the problem persists even at a new save, do let me know, I'll try to cook an early patch for you.