That's what I figured, but for my first playthrough, I was lazy. XD Changing the recipes or something might be a good way to go. As a thought, what if the quests were as follows:
The quest to make the bee either takes you through steps to get the proper bee (detection: meadows/forest, then detection: common, then detection: cultivated, etc.) or it's just a detection of a number of the drones for the actual bee. (Detection: 8 Ferrous Drones.) That quest gives you a fairly simple reward (maybe a sieve and automation upgrade or something, so you can produce a lot more of the resources), and also opens up a repeatable quest to use the nuggets to "buy" pure bees of the same type (consume: 128 iron nuggets to get a reward of 1 ferrous princess and 1 ferrous drone), so that if you do something stupid, like fall out of the world with your bees, you can get more with relative ease.
Of course, all this is just a rambling suggestion. I haven't put nearly the amount of thought into this that you have, and could be going completely the wrong way with it from what you intend.
The quest to make the bee either takes you through steps to get the proper bee (detection: meadows/forest, then detection: common, then detection: cultivated, etc.) or it's just a detection of a number of the drones for the actual bee. (Detection: 8 Ferrous Drones.) That quest gives you a fairly simple reward (maybe a sieve and automation upgrade or something, so you can produce a lot more of the resources), and also opens up a repeatable quest to use the nuggets to "buy" pure bees of the same type (consume: 128 iron nuggets to get a reward of 1 ferrous princess and 1 ferrous drone), so that if you do something stupid, like fall out of the world with your bees, you can get more with relative ease.
Of course, all this is just a rambling suggestion. I haven't put nearly the amount of thought into this that you have, and could be going completely the wrong way with it from what you intend.