That said I see lots of language threads and guides everywhere that talk about all the polite things to say, but no really clear "for dummies" about what they would consider good behavior. A lot of it sounds over-the-top to me, are we over-reacting and being too polite? are they holding us to a higher standard for "intruding" or is the very high level of politeness they exhibit actually normal for them and their just used to it?
Saying, "sorry for shouting" before every shout would just seem insincere over here, but I hear it's rude to just shout over there without prefacing with a quick "Sorry/excuse me."
Is this really true?
For the most part, it's kind of a conditioned thing to do. Like saying 'thanks' when someone holds the door open for you, but you're not actually thinking about how much you appreciate their act of kindness. When they preface their shouts with "sumimasen" it's not that they're necessarily sorry about making you read their text, it's more of a way of politely getting your attention, like saying "excuse/pardon me" to a stranger. I think the reason we sometimes look at that funny is because most Japanese players tend to carry their real world mannerisms and politeness into the virtual world, whereas that's less common with Western players because we're more worried about efficiency and getting to the point. We tend to think of each other as equals on some level (not necessarily in terms of skill), so that we are automatically comfortable speaking with each other online. However, the idea of being unequal and putting yourself below others is so engrained in Japanese culture that it's not surprising to see it carry over into the online world.
Example: JP players don't refer to each other by character name in a party, they refer to each other by job and race. Calling someone by name in Japanese carries the implication that you are close friends, so if you aren't, that's considered surprising/rude. I was in a party once with a Japanese player, he was a Taru PLD. He was very nice and did a good job, and the other party members were using Auto-Translate to compliment him, but they repeatedly referred to him by name. After awhile, it was easy to see that he felt uncomfortable, but reacted positively when I'd refer to him as the PLD. As you might expect, he didn't complain at all, but none of the other party members understood when I tried to explain it. That makes sense, because we look at it in the opposite way: calling someone by name is friendly, but referring to someone just by their job sounds kind of cold and impersonal, like they aren't an individual.
The reason there is no "for dummies" guide on how to behave appropriately in Japanese is because of the above example. Using the language politely is one thing, but understanding all the cultural nuances and social rules that govern how they interact requires a lot of effort. You're pretty safe if you stick with canned phrases, but attempting to go deeper carries stronger ramifications if you get it wrong, and they will
test you to see how well you understand. To further complicate things, Japanese have very mixed feelings about Westerners trying to appeal to them. From what I've experienced over the years, most of them react positively when you use polite phrases, even if they seem like overkill to us, because it shows that you're making an effort to connect. Some of them react very positively when you follow along with those social norms, because it shows that you have a deeper understanding, but there are those who feel offended by it, because they take their culture to be a very personal thing that they are very uncomfortable with sharing. Then on rare occasion, you'll get a JP player who gets offended if you even type something in Romaji, either for the aforementioned reason, or sometimes even out of fear.
Overall, Japanese players know that we can be very pleasant to get along with, but they also know we are capable of extreme rudeness that goes beyond anything they would even think of expressing to their worst enemies. Some just don't want to take the risk of getting partnered up with a rude NA player, because the odds of one of us being rude are sadly quite high. While a good majority of them understand some of the fundamental cultural differences between us, some of them are too uncomfortable interacting with a culture that is strange to them; conversely, others are excited and eager to jump into our parties and experience our alien mannerisms first-hand. But really, it's the same way with us. There are Westerners who are (over)eager to get all friendly with the Japanese, and then there are those of us who don't want to be bothered even trying to use the Auto-Translate.
In the end, all you have to do is recognize that regardless of culture or region, people's personalities cover the spectrum.