Whoops, Charlie, you were posting as I was writing my last post, so I missed this:
Charlie wrote:
“As for sealing the bore, does anyone seal ONLY the bore?”
Yes.
“I know Ralph Sweet soaks his flutes in tung oil; most Baroque makers also seal the whole flute.”
Define seal. If you mean seal as in completely waterproof, then I’d say most of the Baroque flutes I’m aware of are NOT “sealed”. Many makers do oil with polymerizing oils alone, however rarely is the finish that is built-up completely waterproof, or highly durable. I’m not suggesting this is either good or bad.
“It’s a helluvalot easier to dip or soak a flute than to somehow spray something only on the inside. It’s also easier not to mask the outside when soaking it.”
You assume facts not in evidence my friend
Perhaps it’s not done either way? 
"As for why to seal it, it’s so that you don’t have to worry about situations such as the one you’re facing. I’m not crazy about it, because it means that none of your breath is absorbed; every bit of water vapor in your breath condenses in the flute.[/quote]
That’s true. A disadvantage? Perhaps. OTH, a flute with a sealed and smooth bore can be given a quick flick (make sure those corks are tight!!) and the moisture will fly right out - making you plenty of new friends at crowded sessions. An unsealed bore, will absorb some condensation, but you’ll still have plenty of build-up, and swabbing is really the only way to get it out. That said, I’m not at all suggesting this is a serious reason for considering one type of finish over the other. Durability, and the fact that your bore will remain smooth and maintenance free (keeping the tone consistent), are what I would rate as the big advantages to serious bore sealing.
Final note, sealing the bore DOES affect the tone and response of the instrument, much the way lining a headjoint affects those same qualities.
Loren