Let's say that someone has encountered a number of phenomena that they believe demonstrate the existence of God. One counterargument to their reasoned belief in God would be to point out that they have misconstrued the causes of the phenomena...Yet he has come by his knowledge in the same way we come by knowledge of anything that is outside of ourselves in the world.Absolutely, boss. But the quality of that evidence is the thing I always want to examine. (Chesterton makes it impossible because, after a book of build-up, he won't even say what that evidence is. But that is another story.) Putting it that way blurs the distinction between evidence of different quality (per Chesterton again, between the kind of man who doubts the existence of God and the kind who doubts the existence of cows).
So your objection, and Tom's after a fashion, is that you want to say that 'well, we can't have perfect knowledge of things outside of us, but we can have approximate knowledge' -- knowledge on a scale, as Tom put it. The problem is that doesn't get off the ground. Everything you think you know about the outside world is phenomenal (Kant is arguing). Every experience, every sensation, every fact you think you know is actually just a fact about your own internal thoughts...Not so. The perceptions I get are evidence about the external world. "Direct" in the legal sense; "indirect" the way you say Kant's using it. The things I experience are consistent in such a way that they back each other up, and are evidence for each other. I see what looks like a fire; I feel the heat from it; I touch it and get burned by it; I hear and read about it. This is all evidence that such a thing as fire exists. It would be different if I lived in a world where I saw things that looked solid, but my hand passed through them when I tried to touch them; or things that looked just like fire sometimes burned and sometimes didn't for no apparent reason; or I felt my skin was crawling with bugs but everyone else said I was suffering from delusional parasitosis. Those situations would be evidence that my senses were not reliable and that the knowledge I got from them was not so useful.
I'm not in a world like that. The evidence I get runs the other way - within limits. Yes it is possible that this is all a great self-consistent illusion of the brain-in-vat variety. But, I have to say, so what? What difference does this make to anything I have to do? Why paralyze myself by claiming, "This evidence isn't perfect; it could be all wrong without my knowing, so I'll declare all my knowledge completely nonexistent, without value, not knowledge at all?" It's the only evidence I've got and I'll take it as far as it seems to get me. Any map that I carry is not the same thing as the land it represents. It's only an indirect representation, and by its nature imperfect. Do I throw it away? Declare it's no map at all?
Stephen Donaldson's Thomas Covenant - the protagonist of a few trilogies he wrote - was in a similar situation. He kept being transported to a fantasy world, which included a villain named Lord Foul, and (at least in the first two I, which I read) never seemed certain whether he was really visiting another world or dreaming the whole thing. But, he figured, whichever way it was - he was going to fight Lord Foul. I don't understand any other approach.
 I'm partly color-blind and accept there are things you can see that I can't; I can be fooled by optical illusions and know that what I think I'm seeing isn't always quite right.