I don't appreciate the tone of your first post, candy2012. Please assume that if I release a plugin, it will do what it says it does -- with the exception that, like any software, there may be some small bugs. I'm aware of a few with Welcome Pack, for example, but haven't had any time to investigate them for quite some time.
The %s and %d (and others) are tokens used by the printf series of functions, across many programming languages. For PHP's documentation, check out http://uk3.php.net/manual/en/function.sprintf.php As angslycke says, they are used so that the code can figure out where to put certain phrases; in this case, names or keywords or links.
Replacing %s with %2$s or %d with %s, or adding addition symbols, will probably break the string replacement. This is obviously not a great situation, and is fragile, but it was shipped intentionally (otherwise it would have taken a long longer to get the version of the plugin out). To be honest, it has actually been a lot more robust than I originally envisaged.
Eventually, I want to have some sort of drag-and-drop replacement so you can drag in certain 'blocks' that are replaced with a name, or a link, or whatever pre-set piece of data it is. I do not believe I am able to practically do that until certain changes are made to the way BuddyPress (and perhaps WordPress) manages sending emails.
I think I have a ticket on the BuddyPress trac about this (http://buddypress.trac.wordpress.org/), but I can't find it quickly.