First one: "I'm two pages in and I still have no idea what you are saying"
Second one: "I'm in two pages and I still have no idea what you are saying"
The first is idiomatic, and what most native speakers would say.
The second can be misconstrued as "I'm inside two pages", and although that doesn't make sense, it means you have to re-read in order to get the correct interpretation.
Basically, the first one "I'm two pages in" is short hand for "I'm two pages into the book". Which is shorthand for "I have read two pages of the book". It's not, to my knowledge, 'correct' but wouldn't be frowned on and makes sense.
The second example is grammatically correct but does not mean what you want it to mean or make sense logically. It would mean that you were physically inside of two pages.
The reason that you can't switch the location of 'in' in your examples is because you are using it as shorthand for something else.
The others have explained plenty about the meaning of "I'm two pages in", but nobody (IMO) has really dealt justice to the second one, "I'm in two pages".
This probably relates to other instances of similar phrasing, for instance, "the main cavern is in a quarter mile", or "the USB connector should be in ~7/16 inches".
I'm not exactly sure how this relates, but this is what I know about it.
For the second sentence ("I'm in two pages"), the meaning I get is that of, say, a collaborative paper; e.g., "I wrote some of the text on pages 7 and 18." However, it's still a bit clunky -- in that context, I'd be more inclined to say, "I'm on two pages."