“Them” being what, exactly? There are major vocabulary issues here.
What’s an “outset” in this context?
The empirical predictions come from mechanistic hypotheses. In biology, models help in refining and testing hypotheses, but they are not at the center.
The statement “All models are wrong, but some are useful” isn’t a joke. For example, I can model population genetics by blindly drawing marbles if I don’t understand basic probability. That’s precisely why Behe crows about having a model, and never mentions any hypothesis.
You started by defining “hypothesis” as untested, which is utterly wrong with no gray whatsoever, so now you’re jumping to “theory”? Oh boy…
The hypotheses are crafted to be mechanistic and to render testable, empirical predictions.
Very few hypotheses become theories, which is what we call them after they have a long track record of successful predictions, with iterative modifications less “crafted” and more responses to the data, with far more craft going into designing clever experiments that rigorously test those predictions. I’ve only had one epiphany in my career relating to “crafting” a hypothesis, but I assure you it was entirely driven by thinking about and discussing the bewildering data that I had produced by testing my initial (wrong) hypothesis.
I don’t know what your field is, but I’m afraid you’re not really speaking the language of biology here. If the abstract or specific-aims page of your US NIH or NSF grant application started with, “I (we) have crafted a theory,” few reviewers would bother reading further before chucking it in the triage (unreviewed, bottom-half) pile.