One of the tricks I use for breeding a pure line with all the mutated (i.e. bee specific) traits is to breed the common/mundane bees until I get several half-breed cultivated drones (of if lucky a pure bred drone), and a half-breed cultivated princess. Once I have a princess and a drone that have the mutated strain (cultivated in this case), I breed those together and hope the RNG likes me. If it does, I end up with a pure breed strain along with the desired traits, if not, I can try cross breeding the other half-breed strains and hope I get what I want. If not through luck, then through brute force. You can use soul frames to increase the mutation chance.
A good tool to use with this is the apiarist database from extra bees. Once you discover the strain, you can use the database to show you all the natural traits of the bee. Then you can see if you really care about the new traits or not and breed accordingly.