Yeah, this was the big step from Kant to Hegel, the realisation that the object is actually totally inside the subject and vice versa. Unfortunately, when the subject and object get totally mixed up in that way, the philosophy seems to become much more difficult and complicated. Kant's Transcendental Idealism is really useful and easy to understand, but if you want to go a step further into what you describe then it's like moving from Newtonian gravity to General Relativity. Literally everything becomes way more difficult.

I don't think it does. Humans are agents within reality and have perceptions of reality. Your brain having a representation in this reality that might be different from 'true reality' doesn't change the argument at all.

I don't see how your perceptions can be anything other than a direct experience of reality interacting with itself unless you imagine that your mind is separated from reality somehow

We do have a direct experience with reality, but we are only capable of processing an approximate & infinitely simplified model of it.

When you take a picture of an apple, you have a picture of an apple, not the apple itself. Both are real and related, but not the same thing.