This completely depends on what deck you are using to lay off… many of the expensive rental decks can add pulldown via hardware as you export to tape…. but this is tape deck dependant… not FCP dependant.
I’ve had a similar problem before.. is the video black… or all kinds of crazy pink and purple nonsense??? Either way try getting an older version of the Decklink drivers… I’ve had to go back many versions before to get it to work correctly.
yes you can key through water… but to tell you it would work right without being there on set.. impossible… that’s why people hire VFX supervisors… such as myself 😉
Save it out as an animation compression QT movie with an alpha channel… that’s what I’d do… let with the web guys deal with it after that…. there are a thousand ways to deliver this with an alpha channel… but unless they can be more specific.. that’s about as universally accepted method as you will find.
If you have audio in your timeline the couple seconds it’s taking is to render the audio before it renders the video… if you don’t need it turn off the speaker on the offending layer.
This question is not possible to answer until you post a little bit about it’s final deliverable format.. will it be in Flash with an alpha… embedded movie… does it need to respond to clicking in flash… are you adding the background… will it be added later???