I know next to nothing about the mechanics involved, I just have one question.
Can you not simply scale up your production with more machines?  If that's the case, there's not really a fundamental design problem here.
		
		
	 
Yes, you def can scale up, to a certain degree.  But when you go to inoculate a bee larvae with new traits, that process takes 10 minutes per trait... and if you're doing a full 13-trait bee (using the new "serum array"), that means one drone takes 130 minutes to make...  which is almost LOL long... similar to Steve's Carts when you have to wait 2 hours to get the darn train you just made.  And you only get ONE drone, not even a princess!  LOL
I've been able to avoid using 13-trait serums.  I made a "Super Bee" with all the best traits on it, but I did it one trait at a time.  Still, if you only try to mutate one trait, you still have to make like 4 drones because 2 isn't always sufficient (theoretically you'd only need 2 drones to make the mutation, one to change the active and the other to change the inactive trait)...  so you need to wait 40 minutes to get those 4 drones (10 minutes per inoculation to get a larvae).  If I had 4 machines going, then 4 drones would only take 10 minutes total.  So scaling up is def a good option for this specific operation.
But we always knew Binnie's took a long time, nothing has really changed much.  I like what Binnie did with his mods, I give him a thumbs up now that I've spent time working with Genetics.  Won't be long now until I have most of the good, productive bees going.
The first bees I made were Sugary (for sugar) and Agrarian (for wheat).  Kind of odd choices for my first bees, but Genetics requires a decent amount of each item to get started.  Bonemeal too, but I had plenty of that from my Cursed Earth mob grinder.  But I like the fact that sugar and wheat are in demand, because those were two items that I basically never needed before.  I'm glad he added in the whole Incubator line of machines - I think I have 7 of them running (a lot of new items added - a few types of bacteria fluids, growth medium, enzyme, etc), speaking of "scaling up".