That is something annoying, but does this external modifier also includes inoculators with speed serums?
No, it includes only external modifiers (frames, mutator), but not bee-traits (speed).
EDIT: also, in what way are those numbers mesured? Do frames or mutators got a set value? I know they have set value increasements in production and mutation.. But not how to compare to those numbers
You just multiply (!) those numbers and compare them to the limit. I.e. with 3 impregnated frames, you have a production modifier of 2*2*2 -> no risk of losing the bee. With one mutator with uranium and one soul frame, you have a mutation modifier of 10*1.5 = 15 -> too much, your bee may die. I think the limits are 16 for production and 10 for mutation, but I'm not 100% sure.
Question, is this editable is the config?
You can set the beekeeping mode to EASY, this should remove the chance of your bees degenerating.
EDIT: Actually, easy beekeeping mode still lets bees degenerate; it just makes degenerated princesses life forever, like natural ones. That means that there is currently no config option to disable this, but if you only ever play on easy beekeeping mode, it does not matter.