Forestry is a combination of Mendelian Genetics, and a custom "species" mutation mechanism. In conventional genetics a "species" would be a cluster of traits, in Forestry the "species" is simply one of the traits.
If you have bees with traits you are trying to optimize, and you wish to ignore Forestries mutation mechanisim, then you would use a Bee House as In a Bee House there is no chance of mutation.
Pure mendelian genetics means that for each trait (such as species, range, flower etc.) the princess has two options "A" and "B" and the drone has two options, "C" and "D" - all the children will have random combinations "AC", "AD", "BC" and "BD".
So, given your "Mystic|Common" princess and "Mystic|Common" drone, the princess and any drones produced will choose randomly: "Mystic|Mystic","Mystic|Common","Mystic|Common","Common|Common".
So a 1/4 chance of getting a pure Mystic or Common, and a 1/2 chance of getting a hybrid of Mystic and Common. (Which one will be dominant is unclear and possibly random, but Mystic (common) and Common (mystic) are essentially the same thing.
Now, if bred in a Apiary, your given hybrids have a chance to trigger a mutation, which will randomly replace a half the trait options with options associated with Diligent - including one of the species options.
So a Mystic|Common princess with a Mystic|Common drone in an apiary will produce offspring with the following chances (assuming that most mutations have a 5% chance of being triggered):-
1/4 Mystic
1/4 Common
~45/100 Mystic|Common
~2.5/100 Diligent|Mystic
~2.5/100 Diligent|Common