As it is currently, anybody with little to no bee experience can breed very high tier bees within an hour, such as Withering or Diamond. What I would suggest is use something along the lines of Royal Jelly, at a small item-to-mutagen rate. What would be even better is create a new line/species of bee that produces something like Mutagen drops that you can turn into liquid. The Labware should also require something harder to get.

This mod was meant to remove tedium and time sinks from the bee/tree breeding process, adding them back in a different would be counter-productive to it's goal. Most of the things you suggested can be edited in the config if one desires for his server/world.

Besides, i don't think the bug tracker is a good place to discuss balance, the forum thread would be better where other users can weight in, this is not an actual "bug".