I believe (and hope) that Elfman hasn't even begun to discuss this with Burton. He's probably been working on his own music, as Burton wants, and they haven't gotten around to discussing the overall musical picture - which would probably include, at least, the main theme. I can't imagine a director making a character look so much like the original, including an obscure character, including 4 members of the original cast, and recreating an original photograph, and then ditching one of the most important elements of the show. From what we have seen so far, it looks like Burton is trying to make his own vision of Dark Shadows, while maintaining strong connections to the original vision (on a surface level).
Of course, a lot of this could go back to Depp. Depp could have decided how he wanted Barnabas to look, etc. If Depp doesn't provide input on the music, it may very well just be up to Burton's discretion. But, let's hope that Burton decides to keep this consistent flow of original homages throughout.
Plus, if it has become common knowledge (spread by, at least, three very influential people in the Dark Shadows community) that the theme would be used, you would have to assume that this generated from someone with a big say in the matter. Like I said, it doesn't look as if Elfman has discussed this very much with Burton. And, perhaps, that is why we have these conflicting reports. Just speculation on my part, and hopeful speculation at that.