FYI, my AA game name is {DO}Rigel. I'll do my best to cover all the bases here
You can chat in game the with T (say) and Y (say_team). The first is broadcast for everyone to read, the latter is just your team
When a player connects, but doesn't join, there is a message in the console "PlayerName has entered the game." When he/she selects a team, the console reports PlayerName has joined the Red/Blue team.
When a player disconnects, there is a message in the console that says "PlayerName disconnected"
The only way to change teams is to reconnect
You cannot change your name/skin/model, etc in the middle of a team game, you must do it before you join the game. FFA games you can change your player name/skin/model, etc at anytime
You can change a map with rcon or with CallVote
You can start a round with rcon startmap mapname
The only way to end a round is with the server cvar fraglimit and timelimit, these can be set with rcon or with CallVote
Mutators can be set with rcon, but this can be tricky. If ctf is set to 1, and you want to make it instagib FFA, you would have to use rcon to set ctf 0 and set instagib 1. You have to reset the cvars that were previously used or they will retain their value, so you might end up in a a ctf game in insta mode. This is true for dmflags and all cvars that have been set.
Team damage can be turned on and off via dmflags which is set in the server config. That can be changed with rcon and then startmap. There are 2 sounds that play when you damage another player (or your own team if team damage is on), depending on the amount of damage.
There is a scoreboard that dispalys at the end of the round with the scores
I don't know about bomb events, I think that is N/A for us (doesn't matter its not required)
When you capture the flag, there is a message in the console
CallVote supports the following: Kick, Map, FragLimit, and TimeLimit
You can use Rcon to send a message to the game from the console, it will read "Console: MessageTextHere." You cannot send a message this way to one team (and not the other) and you cannot send a message to 1 player. Everyone sees the message, that is the only console chat option available currently.
You can kick a player with rcon kick PlayerName
You can ban a player with rcon sv addip ##.##.##.## that will last until the server is restarted. You can make a ban permanent with rcon sv writeip
You can remove a ban with rcon sv removeip ##.##.##.## this will last until the server restarts, unless you also use rcon sv writeip (I believe, not 100% sure)
Bans are stored in a config file that is executed from the server config. Using sv writeip causes the current filterban to be written to that file.
The only way I know of to change to the "next" map in the list is to print the list with rcon sv_maplist, and then rcon map MapName (where you manually specify the map that was next in the list). There is no rcon NextMap cvar that I am aware of.
You can see all the maps that are stored on the server with rcon dir map/*.bsp
You can get information on the servers config with serverinfo and more with rcon serverinfo
In AA we have clans specified with a clan tag in the player name. The game code doesn't do anything with that, there are no management features for clans or guilds, or what not. That's all done separate from the game code by the players with tags appended to the name.
There is a stats server which maintains statistical information on a player, which can be viewed in the menu browser if they player is connected to a server and you click his/her name. That stats are password protected.
The names PlayerName and playername are considered to be different names. If 2 players try to join with the same name, a digit is applied to the end of one: Player, Player1, Player2, etc. Separate stats are kept for each of the "Player" names based on their password, set in the player setup menu. It does not matter if a digit is applied to the end of their name because there is another person using that name on the server.
Rcon status will provide a list of players, each will have a unique number starting at 0, sequentially as they join.
We do not use PunkBuster or any other cheat inhibitor. We are a tight community and we ban players caught cheating. They get banned from servers, IRC, and the forum. We take cheating very seriously. There are occasional cheaters, and they don't last long. We will allow a player to redeem themselves after being banned, but it is rare that a cheating player will do what is required for that - admit and never ever do it again.
I think for the most part we are compatible, however there may be a few little details that need attention, like selective console chatting. I think we might be able to add this kind of functionality, but it will take me a while to get it into a released version.
I run a modified version of AA on my servers. By this I mean only slightly modified. Many of the mods I started have been adopted by the official game code. I think I can get mods to the rcon chat to player, etc, in the official code (if and when I am able to make them). I don't think I can get the game developers to add this themselves, they are very busy with other projects and we are short handed. However, I say this with a big "I think" because you never know until you ask them, they might jump on the idea of adding B3 support right away. That would be best because my programming skills are limited to say the least.
Let me know if I've missed anything. I had a friend wake me up in the middle of the night (3 hours ago). He wanted me to talk to a player using foul language and making threats on my server. I spoke to the offending player several times, and then started kicking him (also several times). Finally I ended up banning him which will last for 1 day when the server restarts. Next he gets banned for a week, which I must administrate manually. Finally, I will ban him forever if he can't get it together. B3 would help me sleep better

Honestly when I found this, I was so excited, I very much hope I can use it.
I have an eggdrop (IRC bot) that I keep in my clans IRC channel. I have added many TCL scripts and written a few of my own. To be able to do this with a game bot... well... that would be awesome! I mainly want to keep a handle of foul language, and team pests who sabotage and obstruct. CallVote isn't really capable of doing this.