Or should the notification window be disabled if you are actually in Tweetdeck??

Actually, the notifcation focus needs to be rethought entirely.  I have to shut TD completely off when I play games that run fullscreen because the notification windows starts to fight for control if it is left on.  It interferes with game controls and causes graphics trauma in the corner the notification resides in.  A logic call on the active progam needs to be inserted in the routine for the action needed when the notification window triggers.

If the main TD window  is active, then display and sound as determined by settings but do not seize or retain focus.  Most games include indicators that disallow screen savers or the windows key from intercepting control, TD can hopefully implement some system to recognize that in these instances to only allow the audio notification (if indicated by settings).

Other programs in particular that probably should be considered for inclusion in customizing the notification action(s), word processor and spreadsheet programs (i.e. - Word, Excel, etc), E-mail programs when composing messages, programs that reduce or eliminate interaction with he desktop (media programs running movies in fullscreen, slide show or Powerpoint presentations, etc.

I like the new feature of being able to see the content of the alert if I choose, but then I should have the choice of it not completely taking over control while alerting me.

Every other notification window I've used (on Mac or Windows) does not cause focus to change to another application from the notification window.  For example, if I'm in Safari and I press the close button on a notification window from FireFox about a download completed, FireFox does *not* come to the foreground.

Hovering the mouse over the notification window, clicking the close button, or performing any other actions like tagging a tweet as a favourite, replying, adding user to a group, etc. should not bring the main TweetDeck window to the foreground.