There are two basic concepts represented by an auto-map:
1) your character's detailed notes and measurements of their surroundings - cartography mostly represents that okay, but somehow fails to feel right on the detail level progression (I, personally, would sketch rivers and roads pretty quickly as distinguishable things - and I have had 0 levels of cartography training - my map, instead of having very detailed walls describing where I cannot go in a forest, would probably just have a bunch of tree sketches surrounding a rough road sketch). Cartography also breaks here in a way I (and many others) have reported as a bug (which is apparently too big of a bug to fix in this engine, sadly) - which is that if I had a good map of the next village, I would not start erasing features of the map with my inferior mapping skills.
2) your character's memory of their surroundings - part of playing a computer RPG is that you're playing on behalf of someone who lives in that world. Part of the computer's job in the RPG is mediate the transfer of knowledge that should be second-nature to the person living in the world to the player, who hopefully does not live in that world. If you were me, you would not need to consult a map to get to the local QFC - you'd just know. If you were playing a role-playing game where I was the character, you shouldn't have to explore to find the QFC, because I just know. At the start of Eschalon II, you have lived in that village for some time - but have no memory of where anything is? How can that be? The auto-map does not represent memory very well - it only vaguely works when you explore outside the village to places you have plausibly never been before in your life. But only the first time you go there - I can vaguely remember some details (mostly big features like roads and major stores) about places I have only been once (provided I've been there recently).
To represent memory and note-taking better, it would start with major features "this is the river," "this is the mayor's house," "there's a big road from the mayor's house to the blacksmith." And higher levels of cartography would start to fill in details "and the mayor has 3 trees between his west wall and the river," "there's a small dirt path from the blacksmith's to a clearing".
This representation is probably not technically feasible as a programming task, however. The compromise provided by most modern games is to err on the side of your character's memory being good and provide a free auto-map - your character won't forget the village he lives in, and the game is there to provide the knowledge to the player that the character already has.
The compromise provided by Eschalon is to treat your character like a complete idiot who forgets his way to the bathroom unless he takes notes - and his notes leave out important details like roads and rivers until he gets "good" at taking notes - and he will erase any notes magically made for him. That compromise seems to work for some people because they can get free skill points by leaving your character with a short-term memory problem and allocating those points to weapon skills, and offload all the memory and note-taking tasks that should be part of the game (in as much as the game represents your character's knowledge and abilities and mediates them to the player) into the player's hands.
Despite my use of the word "idiot," I think Eschalon's compromise is just fine because it reflects really, really, really old school RPGs where there simply were not resources to represent character knowledge of terrain and I had to draw maps on my own, anyway. The reason I'm writing, then, is not to degrade Eschalon's system, but to compare the reasoning behind it to the "rival" compromise chosen by many modern RPGs - the one that takes character memory and incorporates it into the game, at the cost of turning your character into Captain Eidetic.
Both compromises are dealing with the core issue of "actually realistically representing memory (supplemented by in-game note-taking) is really, really, really hard." Both compromises have their good sides and bad sides. Nobody is an fool or wrong-headed for wishing the game chose the other compromise, but no one is a fool or wrong-headed for supporting the current compromise, either. What you need to realize, then, is that arguing over which compromise is better is pointless - neither is true to character memory (the character should neither be a complete idiot about their surroundings, nor should they have perfect memory of their surroundings).
I think that's mostly what I want to say. I'll probably get "tl;dr" on this, and I imagine people will cherry pick sentences and miss my entire point, because that's the nature of posting on the internet. I can live with that, but here's the summary: "there is no realistic automap feature to be found in any game in the near future. There are two systems, neither of which is perfect, and BW has chosen one of them. If you like the other one, that's fine for you, but unlikely to change Book III since BW is unlikely to majorly rewrite core mechanics. There is no real argument to be had with people who like the other system - it's just a matter of opinion."