The Chantry teaches that free will exists. So while the Maker is omniscient/omnipotent to a degree, he still exists in a world with free will. Theoretically, like many omnipotent Gods in religions, he could overturn free will if he wanted but chooses to allow it. For whatever reason. The Chantry teaches that the Golden City was turned black by Magisters who, in their pride, sought to become Gods. The Maker allowed this to happen and could theoretically "reverse" it but he will not - according to the Chantry - until all the people (and other races) of Thedas accept him as the one true God. Hence all the Exalted Marches. Now, the religion clearly rests upon its laurels and few seem to be actually trying to convert a bunch of other people for the Maker's favour at the moment. It's more a tradition than a true cause for most. They're busy with their day-to-day human problems and power struggles, after all.
You could be right, of course, and this could all be a grand plan, if the Maker is real. But there could be any number of "truths" possible. Assuming the Maker a) exists and b] is truly a God.
I'm pretty sure BioWare hasn't decided if he exists or not.
But so far they're leaning towards "every god is real, except the Maker".
Yeah, but all those gods who are "real" are also not really gods (in the sense of the Maker or what many would consider a God) - just very powerful beings. They didn't create the world; they don't truly rule it. They were merely semi-immortals with power.