Jackinyourcities: Hi! Welcome! To answer your original questions:
1. Yes, there are a few things different from the rulebook that I noticed after joining. Firstly, you can conduct diplomacy during the retreats/disbanding and building/disbanding phases. See this discussion:
threadID=463373. Secondly, you should note that "civil disorder" in the rulebook ≠ "civil disorder"/"CD" that is used on this website. The rules for civil disorder are implemented the same, but the term on this site refers to two consecutive civil disorder phases for a country, which is important because that's the point where other people can jump into the game and take over the absent players' positions. See this discussion:
threadID=473713. (There was also a problem for a couple years where the order of civil disorder disbands was skewed, but I think that that issue has been resolved.) Finally, don't take the markings on the map or annotation in the Orders Archive of your game to seriously. The resolution is always accurate, but how that resolution is depicted is not always accurate. See this discussion:
threadID=494283.
2. Yes, the difference on this site is that it's always better. The points system, by the way, is your only incentive to take over positions that are in "CD" and the best way to measure your success when you do. The "Game stats" on your profile page and the Ghost-Ratings system mentioned above both penalize you heavily for doing so. See this discussion:
threadID=458170. By the way, what website did you come from?