I think that's likely. ME drops you off there for check-in, and then you have to take another bus to get to your actual room. When you stay there, you never come back to custom house unless you have to. (There's a desk at Old Port Royale for most inquiries.) And then you have the same issue when checking out - having to get back there. It really would make more sense to have all this at Old Port Royale. However, because the resort is so spread out, anywhere you put the main lobby would still run into a problem of needing busing to the various areas - they would need an expanded space there to fit the check-in stuff.
Assuming it is a DVC construction, I think it's a good assumption that the check-in location would be moved.