[Avodah] bee honey and davar hamamid/non kosher enzymes logically coherent?

[Shaya Potter]

Is it possible to present a coherent logical system for why bee honey
is kosher (per hazal) and there's a concept of davar hamamid when it
comes to kashrut (which I have been told is more of a concept from the
rishonim?) and in modern times (and even before re rennet and cheese)
this is applied to enzymes which have a large role in industrial food
production.

Now, the concept of davar hamamid seems difficult in general from what
I understand the gemara's concept of kashrut is, which is that its all
based around taam.  Davar hamamid on the other hand is that the food
couldn't be made without the item, but it really has no impact itself
on the taam of the item.

Now, we know the gemara allowed bee honey, we also know that bee honey
is produced via enzymes in the saliva of the non kosher bee (i.e. non
kosher enzymes) fixing the nectar the bees get from flowers and
turning it into honey.  How is this fundamentally any different than
using a non kosher rennet (ignoring the rest of gvinat yisrael issues)
to turn milk into cheese?

This is an issue that has been bugging me for a while now, and haven't
heard any answers that I find satisfying.