Mind you i care little for irl religious debate in a fantasy world but find the theories dismissing the Maker's existence just as flawed and inconclusive to any that proves it.
Lyrium, the power of belief mediated through the Fade, those are things we either already know to exist or whose existence is in accord with the lore. Not to make a too fine point of it, but the Maker's existence is not part of the lore, belief in his existence is. Meanwhile, we know that human dreams can shape the Fade. It's absolutely no stretch to think that collective belief may let magical effects manifest, and since the Fade is (to use yet another in-world theory) co-existent with material reality, it touches everything that isn't specially shielded against it.
Furthermore, the problem with unknown agents is that it's structurally impossible to conclusively falsify their existence, so any convincing evidence of their existence can't be indirect. You'd need to present them. Why do you think physicists spent decades and billions in order to find direct evidence of the Higgs boson? They weren't fooling around. The standards of science demanded it. With unknown
free-willed agents the problem becomes even worse. Suppose you assume the Maker exists, how do you know its motivations? I really don't understand why people are unable to see how utterly arbitrary the assumption of some unknown free-willed agent is. You could basically claim anything, and on top of it the assumption explains nothing. If agent X wants something, why? What are its interests, and why? How can its existence be explained? The assumption of unknown free-willed agents makes the problem so much more complex and raises so many more questions than it solves.
Meanwhile - to get back to Thedas - the non-supernatural explanations of Andraste's ashes are just as unproven, but they work with known agents and for that reason are to be preferred unless they run into contradictions. Experiments could be designed to prove or disprove them.
And even that is not the end of it. People accept the Maker as an explanation because the concept is familiar, while in reality it is a concept fantastic beyond anything fantasy has ever invented, a literally world-shattering assumption. What about assuming that this hidden free-willed agent is something like.....Azathoth? May I mention this is just as likely given that we know nothing of the unknown entity's nature and motivation?
Edit:
Perhaps one more example: I guess that if someone claimed "Flemeth did it" this would be dismissed by some as a conspiracy theory. Why then believe in an unknown agent? Isn't that even more of a conspiracy theory?