All theories start as hypothetical. It's the scientific method. Many of the most useful theories have been shown to link different areas of knowledge together. If you think about it, a theory which plausibly answers several questions at once is far more likely to be correct.i just pointed out it was hypothetical.
No theory in the history of science has ever been proven to be correct. Many have been shown to be extremely likely to be correct though, by the weight of evidence. As for disagreement, that's how science advances. Thesis - antithesis - synthesis, which becomes the new thesis, and so it goes on, in a long never-ending chain. That's how a very brainy German once explained it. Design - all kinds of design - also develop in the same way.The problem with scientific theories is, that they are just theories until proven to be correct, and even then there will be other scientists who disagree with those theories and will set out to prove they are right, and it goes on and on and on.