It would depend on your TA, but the big agencies a lot of
DCL cruisers use (Dreams and Costco) have no problem with their clients using the DVA and calling in the payment themselves. They still give the same amount of OBC. I use a TA from Dreams and I just shoot her an email when I make a payment with the DVA so she can update her records.
Yes, it would be the same if you used the credit card. The difference I see is if the timing worked out right, the refund from canceling the package would hit your card in the same billing cycle as your new deposit on the room only so they would somewhat offset each other.
I've never booked a VIP tour before. Do you have to pay the entire amount when you book it or just a deposit? With the DVA it matters when the payment is made, not when the reservation was booked.