I did dump a couple of bees into that system that I didn't want to, but didn't lose them. I was using the metered crate trick that I usually use for feeding endoflames. (hopper into open crate over wooden pressure plate, redstone from pressure plate to hopper, so that it only dispenses when there is nothing left on the ground; and an auxiliary stone pressure plate to stand on while I dump stuff in, so nothing runs until I leave). Any important bees, such as ethereal, used in much breeding, gets a genetic template made and added to a filing cabinet/genetic library. That way I don't have to worry about losing them, and can imprint more as needed.
For this pack, speed was a good thing. A tightly themed pack like this is going to be a bit limited in what you can do within the theme without it getting grindy. I did find it a bit tedious toward the end, though if I'd jumped on the alveary quest sooner, I would have done a set it and forget it submission system for the bulk combs. Instead, there was a lot of idling. Oh well.
Still, I had fun, and it inspired some ideas for the modpack I'm thinking of making (no bees immediately available, but there will be a way of getting genetic templates, and you need a loonium to get the resources to build the machines, mwa ha ha)