I might be missing something but Binnie's new Genetics machines seem just about useless for crossbreeding bees.
With the old machines I'd take a princess, bump her fertility to the highest I had, do the same with a drone I wanted to cross her with, them put her in an alveary with max mutation chance that wouldn't damage bees. Once or twice would be enough to get the cross I wanted, then I'd put the princess and purebred drones in an apiary with automation until she made a bunch of spare drones, then use the spare drones to isolate the genetic traits I wanted from that bee, in particular the species itself.
Can't inoculate princesses at all with Genetics, but even beyond that I've been trying to isolate a bee species gene for over 3 days now. That is 3 real world days, chunkloaded, with the machines running 24x7. Without the ability to isolate the species itself in a timely fashion I can't make a new drone for that species with the traits I want to crossbreed in before going for the next mutation.
With process times like that I think at least when it comes to bees I'm not even going to use the machines until the very end, when I already have all the species/traits I want. Progression through the species has actually been slowed down by using the machines. I could have just automated a bank of apiaries and thrown bees at them until I had the species I wanted, it would have been quicker.