Except I've had this conversation with powercrystals. He said that non-vanilla recipes are designed specifically to be harder, on the presumption that that's the goal of using the non vanilla recipes. Specifically, they are not a "mod dependent / equally hard" recipe, but rather an intentionally harder recipe.

And they are.  A tesseract for 4 deep storage instead of some plastic, requiring both more resources and the infrastructure to make the parts?  Every single machine using a TE frame instead of...some plastic.  Some of the recipes are simply harder in simple differences that would be possible in vanilla recipes.  Both the intent and the result is hard mode.

Note about bees, that ED managed a stable cultivated breed by random pairing.  Meaning he took unanalyzed princess, and unanalyzed drones and randomly paired them together repeatedly.  It's not a difficult process, bees are not hard and only time consuming if you feel some need to stand there and stare at them instead of going off and doing something else.