Unfortunately no. Flash Catalyst only supports the transitions available in the Flex Framework. If you wanted to create more complex transitions, you would need to add them by using Flash Builder and create either the MXML or Actionscript for the effect.
Could I use the third party effect in Flash, create a .swf file and then import it into catalyst?
The effect code would not be accessible to Catalyst. You can use Flash Profession to animate the item with the effect you want, then import that swf into Flash Catalyst. FC does allow you to play and stop a swf.
The imported swf should be published with player 10.1 as the target.
Hope this helps,
Thanks for the information, I'll give it a try