At what stage is this bonus of 100 points is awarded to a new user and what are the privileges that come with it?
When the system feels like it :)
The bonus is only given to people who have already participated in another SE site earning at least 200 rep. This is to shortcut some of the restrictions that are in place to protect against people who just don't understand what the buttons are for. New users are not even allowed to vote up. Without participating a little bit, they figure the work flow might not be clear and allowing non-participants to drive by on the internet and vote/etc would skew the balance of things.
The bonus usually comes in within a minute or two of actually making the association link between your accounts. Once the account are linked it triggers some queue that gives you the extra 100 rep.
The privileges that come with it are a result of the rep, not separate from it so the result is no different than if you'd earned 100 rep through questions or answers. Basically 100 rep is enough to get you chat and comment privs, cut the new user restrictions on posting links, gives you enough to up vote, edit wikis, etc.
You can see the exact privileges that 100 points would bring on the privileges page.